HDAC1

Summary

HDAC1 (histone deacetylase 1, HGNC:4852) is a protein-coding gene on chromosome 1p35.2-p35.1, encoding Histone deacetylase 1 (Q13547). Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).

Histone acetylation and deacetylation, catalyzed by multisubunit complexes, play a key role in the regulation of eukaryotic gene expression. The protein encoded by this gene belongs to the histone deacetylase/acuc/apha family and is a component of the histone deacetylase complex. It also interacts with retinoblastoma tumor-suppressor protein and this complex is a key element in the control of cell proliferation and differentiation. Together with metastasis-associated protein-2, it deacetylates p53 and modulates its effect on cell growth and apoptosis.

Source: NCBI Gene 3065 — RefSeq curated summary.

At a glance

• Gene–disease (curated): congenital heart disease (Disputed, ClinGen)
• Clinical variants (ClinVar): 63 total — 1 likely-pathogenic
• Regional missense constraint (gnomAD): 1 of 4 regions constrained (≈29% of expected missense variation)
• GTEx eGene: eQTL in 20 tissues, sQTL in 2 (q < 0.05)
• Drug target: yes — 2 curated mechanism-of-action drugs; 48 molecules with ChEMBL bioactivity (top 1% of genes corpus-wide)
• Approved drugs (ChEMBL mechanism of action): 1 — Vorinostat
• Constraint (gnomAD): pLI 0.95 (loss-of-function intolerant), LOEUF 0.53 (moderately constrained)
• Transcription factor: yes — 84 downstream targets (CollecTRI)
• MANE Select transcript: NM_004964
• Interaction hub: 5,872 STRING partners (top 1% of genes corpus-wide)
• Notable: 63 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4852
Approved symbol	HDAC1
Name	histone deacetylase 1
Location	1p35.2-p35.1
Locus type	gene with protein product
Status	Approved
Aliases	HD1, GON-10, KDAC1
Ensembl gene	ENSG00000116478
Ensembl biotype	protein_coding
OMIM	601241
Entrez	3065

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 18 protein_coding, 7 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 3 retained_intron

MANE Select: ENST00000373548

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 3, TSL 3: 1, TSL 5: 4

ENST00000373548, ENST00000428704, ENST00000463172, ENST00000471488, ENST00000472928, ENST00000476391, ENST00000481281, ENST00000482310, ENST00000484305, ENST00000490081, ENST00000718279, ENST00000906551, ENST00000906552, ENST00000906553, ENST00000906554, ENST00000906555, ENST00000906556, ENST00000933659, ENST00000933660, ENST00000933661, ENST00000943499, ENST00000973421, ENST00001020943, ENST00001065485, ENST00001065486, ENST00001065487, ENST00001065488, ENST00001065489, ENST00001065491, ENST00001123767, ENST00001123768, ENST00001143399

RefSeq mRNA: 1 — MANE Select: NM_004964 NM_004964

CCDS: CCDS360

Canonical transcript exons

ENST00000373548 — 14 exons

Exon	Start	End
ENSE00001850850	32292083	32292218
ENSE00003469455	32316665	32316782
ENSE00003539653	32324479	32324553
ENSE00003547692	32331676	32331806
ENSE00003550072	32326939	32327077
ENSE00003564227	32329068	32329160
ENSE00003567410	32332701	32332749
ENSE00003578115	32330768	32330908
ENSE00003626458	32327536	32327677
ENSE00003638824	32330578	32330686
ENSE00003657444	32332090	32332242
ENSE00003691785	32331474	32331582
ENSE00003693858	32333017	32333626
ENSE00004034612	32302621	32302733

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 99.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 44.0677 / max 361.9177, expressed in 1821 samples.

Highest expression (Bgee): colonic mucosa, mucosa of sigmoid colon, mucosa of transverse colon, epithelium of nasopharynx, rectum.

Genetic regulation across tissues (GTEx eQTL / sQTL)

HDAC1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 20 tissues and its splicing (sQTL) in 2 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 22 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Artery Tibial	eqtl	4.3e-07	+0.47	1:32333602:T:C
Cells Cultured fibroblasts	eqtl	6.2e-07	-0.56	1:32291945:C:T
Adipose Visceral Omentum	eqtl	1.5e-06	-0.25	1:32250040:G:T
Adipose Subcutaneous	eqtl	2.3e-04	-0.59	1:32291945:C:T
Skin Sun Exposed Lower leg	eqtl	4.2e-04	-0.42	1:31874849:G:A
Muscle Skeletal	eqtl	8.1e-04	+0.31	1:32283609:A:C
Testis	eqtl	1.1e-03	+0.36	1:32333602:T:C
Stomach	eqtl	1.3e-03	-0.47	1:31803084:G:A
Brain Frontal Cortex BA9	eqtl	1.7e-03	-0.55	1:32304778:G:C
Nerve Tibial	eqtl	3.0e-03	-0.53	1:32291945:C:T
Esophagus Muscularis	eqtl	3.7e-03	+0.41	1:32333602:T:C
Thyroid	eqtl	4.3e-03	+0.34	1:32332533:A:G
Breast Mammary Tissue	eqtl	5.6e-03	-0.12	1:31924723:C:T
Esophagus Gastroesophageal Junction	eqtl	1.2e-02	+0.37	1:32725740:C:T
Brain Hippocampus	eqtl	1.3e-02	+0.42	1:32333602:T:C
Esophagus Mucosa	eqtl	1.8e-02	+0.25	1:32333602:T:C
Cells Cultured fibroblasts	sqtl	1.9e-02	+0.45	1:32255796:A:ATT
Brain Caudate basal ganglia	eqtl	2.8e-02	-0.44	1:31876510:T:C
Heart Atrial Appendage	eqtl	3.2e-02	+0.40	1:32272462:T:C
Spleen	eqtl	3.6e-02	+1.20	1:33105655:A:G

FANTOM5 promoters

3 alternative TSS:

Promoter ID	TPM avg	Samples expressed
1979	21.8285	1808
1978	21.2187	1809
1977	1.0204	531

Top tissues by expression

showing 100 of 295 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
colonic mucosa	UBERON:0000317	99.03	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.01	gold quality
mucosa of transverse colon	UBERON:0004991	98.43	gold quality
epithelium of nasopharynx	UBERON:0001951	98.42	gold quality
rectum	UBERON:0001052	98.35	gold quality
lymph node	UBERON:0000029	98.28	gold quality
esophagus squamous epithelium	UBERON:0006920	98.00	gold quality
pylorus	UBERON:0001166	97.98	gold quality
right uterine tube	UBERON:0001302	97.94	gold quality
caecum	UBERON:0001153	97.92	gold quality
transverse colon	UBERON:0001157	97.90	gold quality
gingiva	UBERON:0001828	97.90	gold quality
vermiform appendix	UBERON:0001154	97.85	gold quality
gingival epithelium	UBERON:0001949	97.85	gold quality
islet of Langerhans	UBERON:0000006	97.84	gold quality
epithelium of esophagus	UBERON:0001976	97.84	gold quality
granulocyte	CL:0000094	97.70	gold quality
pharyngeal mucosa	UBERON:0000355	97.57	gold quality
duodenum	UBERON:0002114	97.53	gold quality
oral cavity	UBERON:0000167	97.49	gold quality
small intestine Peyer’s patch	UBERON:0003454	97.47	gold quality
stromal cell of endometrium	CL:0002255	97.46	gold quality
esophagus mucosa	UBERON:0002469	97.46	gold quality
squamous epithelium	UBERON:0006914	97.46	gold quality
right lobe of thyroid gland	UBERON:0001119	97.44	gold quality
thymus	UBERON:0002370	97.43	gold quality
large intestine	UBERON:0000059	97.39	gold quality
gall bladder	UBERON:0002110	97.34	gold quality
colon	UBERON:0001155	97.33	gold quality
intestine	UBERON:0000160	97.28	gold quality
jejunal mucosa	UBERON:0000399	97.27	gold quality
spleen	UBERON:0002106	97.24	gold quality
seminal vesicle	UBERON:0000998	97.12	gold quality
small intestine	UBERON:0002108	97.12	gold quality
left lobe of thyroid gland	UBERON:0001120	97.08	gold quality
right ovary	UBERON:0002118	97.08	gold quality
cardia of stomach	UBERON:0001162	97.05	gold quality
thyroid gland	UBERON:0002046	97.04	gold quality
leukocyte	CL:0000738	96.95	gold quality
body of stomach	UBERON:0001161	96.92	gold quality
monocyte	CL:0000576	96.91	gold quality
left ovary	UBERON:0002119	96.91	gold quality
fundus of stomach	UBERON:0001160	96.89	gold quality
mononuclear cell	CL:0000842	96.88	gold quality
ectocervix	UBERON:0012249	96.84	gold quality
endocervix	UBERON:0000458	96.83	gold quality
metanephros cortex	UBERON:0010533	96.78	gold quality
sigmoid colon	UBERON:0001159	96.77	gold quality
adenohypophysis	UBERON:0002196	96.73	gold quality
tonsil	UBERON:0002372	96.73	gold quality
tongue squamous epithelium	UBERON:0006919	96.72	gold quality
vagina	UBERON:0000996	96.71	gold quality
ileal mucosa	UBERON:0000331	96.70	gold quality
pituitary gland	UBERON:0000007	96.66	gold quality
mouth mucosa	UBERON:0003729	96.66	gold quality
palpebral conjunctiva	UBERON:0001812	96.65	gold quality
corpus epididymis	UBERON:0004359	96.65	gold quality
body of uterus	UBERON:0009853	96.64	gold quality
esophagus	UBERON:0001043	96.60	gold quality
nasal cavity epithelium	UBERON:0005384	96.58	gold quality
stomach	UBERON:0000945	96.57	gold quality
uterine cervix	UBERON:0000002	96.55	gold quality
renal medulla	UBERON:0000362	96.53	gold quality
minor salivary gland	UBERON:0001830	96.50	gold quality
superior surface of tongue	UBERON:0007371	96.50	gold quality
prostate gland	UBERON:0002367	96.46	gold quality
mammalian vulva	UBERON:0000997	96.44	gold quality
saliva-secreting gland	UBERON:0001044	96.43	gold quality
lower esophagus mucosa	UBERON:0035834	96.43	gold quality
cervix epithelium	UBERON:0004801	96.42	gold quality
ovary	UBERON:0000992	96.34	gold quality
muscle layer of sigmoid colon	UBERON:0035805	96.27	gold quality
urinary bladder	UBERON:0001255	96.25	gold quality
smooth muscle tissue	UBERON:0001135	96.22	gold quality
pancreas	UBERON:0001264	96.18	gold quality
right adrenal gland	UBERON:0001233	96.17	gold quality
female reproductive system	UBERON:0000474	96.16	gold quality
right adrenal gland cortex	UBERON:0035827	96.14	gold quality
bronchial epithelial cell	CL:0002328	96.10	gold quality
metanephros	UBERON:0000081	96.10	gold quality
blood	UBERON:0000178	96.09	gold quality
parotid gland	UBERON:0001831	96.07	gold quality
bronchus	UBERON:0002185	96.06	gold quality
uterus	UBERON:0000995	96.04	gold quality
epithelium of bronchus	UBERON:0002031	96.03	gold quality
urethra	UBERON:0000057	95.98	gold quality
mucosa of urinary bladder	UBERON:0001259	95.96	gold quality
mucosa of stomach	UBERON:0001199	95.95	gold quality
endometrium	UBERON:0001295	95.92	gold quality
nasal cavity mucosa	UBERON:0001826	95.88	gold quality
tongue	UBERON:0001723	95.81	gold quality
pancreatic ductal cell	CL:0002079	95.79	gold quality
trachea	UBERON:0003126	95.79	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.78	gold quality
adrenal cortex	UBERON:0001235	95.77	gold quality
left adrenal gland	UBERON:0001234	95.75	gold quality
placenta	UBERON:0001987	95.73	gold quality
lower esophagus	UBERON:0013473	95.72	gold quality
left adrenal gland cortex	UBERON:0035825	95.71	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.70	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.51

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Tonsil	tissue	116.1	high
Colon	tissue	112.0	high
Lymph node	tissue	111.8	medium
Rectum	tissue	101.7	high
Thymus	tissue	96.9
Stomach 1	tissue	79.3	high
Small intestine	tissue	76.1	high
Thyroid gland	tissue	73.4	high
Appendix	tissue	72.4	high
Duodenum	tissue	70.1	high
Esophagus	tissue	63.7	high
Urinary bladder	tissue	59.6	high
Parathyroid gland	tissue	58.6	medium
Spleen	tissue	57.7	medium
Bone marrow	tissue	56.0	high
Ovary	tissue	55.7	medium
Prostate	tissue	54.0	medium
Seminal vesicle	tissue	53.9	medium
Fallopian tube	tissue	53.4	high
Cervix	tissue	53.2	high
Breast	tissue	52.5	medium
Gallbladder	tissue	52.0	high
Placenta	tissue	49.8	high
Vagina	tissue	49.6	medium
Salivary gland	tissue	49.1	medium
Epididymis	tissue	48.6	high
Endometrium 1	tissue	45.0	medium
Smooth muscle	tissue	43.6	medium
Kidney	tissue	41.6	medium
Liver	tissue	39.0	medium
Lung	tissue	38.9	medium
Adrenal gland	tissue	38.0	not detected
Skin 1	tissue	35.9	medium
Pancreas	tissue	34.1	medium
Testis	tissue	33.8	high
Pituitary gland	tissue	30.7
Spinal cord	tissue	29.4
Corpus callosum	tissue	28.9
Heart muscle	tissue	27.2	low
Adipose tissue	tissue	26.8	low
Substantia nigra	tissue	26.1
Superior colliculi	tissue	25.8
Medulla oblongata	tissue	24.8
Midbrain	tissue	23.0
Frontal cortex	tissue	22.6
Periaqueductal gray	tissue	22.3
Thalamus	tissue	22.1
Hypothalamus	tissue	22.1
Caudate putamen	tissue	21.1
Pons	tissue	20.9
Cerebellum	tissue	20.0	not detected
Retina	tissue	17.6
Septum	tissue	16.8
Putamen	tissue	16.5
Tongue	tissue	16.4
Ventral forebrain	tissue	15.1
Skeletal muscle	tissue	14.3	not detected
Olfactory bulb	tissue	14.3
Hippocampal formation	tissue	13.7
Amygdala	tissue	13.5

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Blood vessel (38.1), Dorsal spinal cord (29.4), White matter (28.9), Ventral spinal cord (26.9), Area postrema (19.0).

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

showing 30 of 84 targets:

Target	Regulation
ABCB1	Repression
ADAM10	Repression
ALOX15	Unknown
APOC3	Unknown
AR	Unknown
BAMBI	Repression
BCL2A1	Activation
BIRC3	Activation
BIRC5	Unknown
BRCA2	Repression
CCND1	Activation
CCND2	Repression
CD1D	Repression
CD44	Repression
CD82	Repression
CDH1	Repression
CDK4	Activation
CDKN1A	Repression
CDKN2A	Unknown
CEBPA	Repression
CLDN7	Activation
COL1A2	Activation
CXCL8	Unknown
CYP3A4	Unknown
DEFB1	Unknown
DNMT1	Unknown
E2F1	Repression
EGFR	Repression
EGR1	Repression
EHMT2

Upstream regulators (CollecTRI, top): AR, DNMT1, EZH2, FLI1, GATA1, MTA1, NFKB1, NR4A1, PDGFB, PPARG, PYHIN1, RELA, RFX1, SATB1, YY1

miRNA regulators (miRDB)

Targeting HDAC1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 74 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-4719	99.73	72.10	3329

Functional genomics

gnomAD constraint: pLI 0.95, LOEUF 0.529, missense Z 2.71 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000373548 splits into 4 regions with different missense tolerance; 1 is missense-constrained (≈29% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
1:32,292,170–32,324,482	80 / 126.3	0.63	no
1:32,324,483–32,329,128	62 / 180.0	0.34	yes (p 1.4e-18)
1:32,329,129–32,331,731	105 / 192.6	0.55	no
1:32,331,732–32,333,041	126 / 126.2	1.00	no

Literature-anchored findings (GeneRIF, showing 40)

• Expression profile of histone deacetylase 1 in gastric cancer tissues (PMID:11749695)
• role in regulation of the telomerase reverse transcriptase (hTERT) gene (PMID:11855854)
• Phosphatase inhibition leads to histone deacetylases 1 and 2 phosphorylation and disruption of corepressor interactions (PMID:11919195)
• association with proliferating cell nuclar antigen, integrating DNA replication and chromatin modification (PMID:11929879)
• Counterregulation of chromatin deacetylation and histone deacetylase occupancy at the integrated promoter of human immunodeficiency virus type 1 (HIV-1) by the HIV-1 repressor YY1 and HIV-1 activator Tat. (PMID:11940654)
• Androgen receptor, Tip60, and HDAC1 form a trimeric complex upon the endogenous AR-responsive PSA promoter, acetylation and deacetylation of the AR is an important mechanism for regulating transcriptional activity. (PMID:11994312)
• interaction with large subunit of replication factor C (PMID:12045192)
• associated with silencing DAP kinase gene expression in colorectal and gastric cancers (PMID:12087472)
• HDAC-Sin3A complex regulates LHR Gene transcription (PMID:12091390)
• interaction with mCpG-binding domain of MBD2 (PMID:12124384)
• localization in Aurora-A-positive centrosomes in M phase (PMID:12354758)
• Data show that the adenovirus protein Gam1 counteracts histone deacetylase 1 sumoylation both in vivo and in vitro. (PMID:12393750)
• The HDAC1 complex binds MDM2 in a p53-independent manner and deacetylates p53 at all known acetylated lysines in vivo. (PMID:12426395)
• Che-1 affects cell growth by interfering with the recruitment of HDAC1 by retinoblastoma protein. Che-1 overexpression activates DNA synthesis in quiescent NIH-3T3 cells through HDAC1 displacement. (PMID:12450794)
• recruited by prohibitin for transcriptional repression (PMID:12466959)
• We demonstrate that MI-ER1 repressor activity is due to interaction and recruitment of a trichostatin A-sensitive HDAC1, deletion analysis revealed that recruitment of HDAC1 to hMI-ER1alpha and hMI-ER1beta occurs through their common ELM2 domain. (PMID:12482978)
• Here we show that HDAC1 associates with and blocks Ser133 phosphorylation of CREB during pre-stimulus and attenuation phases of the cAMP response (PMID:12567184)
• histone deacetylase 1 overexpression is associated with advanced stage esophageal squamous cell carcinoma. (PMID:12579268)
• deacetylase HDAC1 acts as an antagonist of the tumor suppressor p53 in the regulation of the cyclin-dependent kinase inhibitor p21 (PMID:12665570)
• We investigated occupancy of ER-alpha promoter by pRb2/p130-E2F4/5-HDAC1-SUV39 H1-p300 and pRb2/p130-E2F4/5-HDAC1-SUV39H1-DNMT1 complexes, and provided a link between pRb2/p130 and chromatin-modifying enzymes in the regulation of ER-alpha transcription (PMID:12789259)
• p52 NF-kappaB subunit associates with histone deacetylase 1 when p53 represses cyclin D1 transcription through down regulation of Bcl-3 (PMID:12808109)
• The MLL repression domain specifically interacts with HDAC1. (PMID:12829790)
• HDAC1 is displaced from the p21WAF1/CIP1 promoter by Che-1 in human colonic carcinoma (PMID:12847090)
• IkappaBalpha regulates the transcriptional activity of homeodomain-containing proteins positively through cytoplasmic sequestration of HDAC1 and HDAC3 (PMID:12972430)
• HDAC1 represses the small GTPase RhoB expression in human nonsmall lung carcinoma cell line. (PMID:13679859)
• HDAC1 has a role in interferon-stimulated transcription and innate antiviral immunity (PMID:14645718)
• MeCP2 acts as a corepressor of PU.1 probably due to facilitating complex formation with mSin3A and HDACs. (PMID:14647463)
• HDAC1 interacts with p300 C/H3 domain. Its overexpression interferes with either activation of Gal14p300 fusion protein or p300-dependent co-activation of MyoD and p53. E1A competes with HDAC1 for C/H3 binding. (PMID:14968110)
• interaction of HPV type 31 E7 with HDACs and the integrity of the zinc finger-like motifs are essential for extending the life span of keratinocytes and for stable maintenance of viral genomes (PMID:15016876)
• HDAC1 upregulated in pre-malignant and malignant lesions, with the highest increase in expression in hormone refractory (HR) prostate cancer; in CWR22 xenograft model, androgen dependent regulation of HDAC1 demonstrated. (PMID:15042618)
• Ezh2 competes with HDAC1 in binding to pRb2/p130, disrupting their occupancy on the cyclin A promoter. (PMID:15077161)
• histone deacetylase has a role in transforming growth factor-beta signaling in breast cancer cells (PMID:15155736)
• Tax interacts directly with HDAC1 and regulates binding of the repressor to the HTLV-1 promoter (PMID:15194748)
• SENP1’s ability to enhance AR-dependent transcription is not mediated through desumoylation of AR, but rather through its ability to deconjugate histone deacetylase 1 (HDAC1), thereby reducing its deacetylase activity. (PMID:15199155)
• stabilization of NF-E4 by acetylation is PCAF-dependent; acetylation of Lys(43) also reduces the interaction between NF-E4 and HDAC1, potentially maximizing the activating ability of the factor (PMID:15273251)
• Accumulation of ICBP90 in breast-cancer cells might suppress expression of tumor suppressor genes through deacetylation of histones after recruitment of HDAC1. (PMID:15361834)
• In prostate tissues, the abundance of HDAC1 protein, which was exclusively expressed in the cell nucleus, was similar in normal and malignant epithelial cells, but was usually lower in stromal cells. (PMID:15590418)
• HDAC1 negatively regulates the cardiovascular transcription factor KLF5 through direct interaction (PMID:15668237)
• plays a critical role in repression of endothelial constitutive nitric oxide synthase gene (PMID:15722551)
• interleukin-5 transcription repression by the glucocorticoid receptor targets GATA3 signaling and involves histone deacetylase recruitment (PMID:15826950)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	hdac1	ENSDARG00000015427
mus_musculus	Hdac1	ENSMUSG00000028800
rattus_norvegicus	Hdac1l	ENSRNOG00000013695
caenorhabditis_elegans		WBGENE00009657
caenorhabditis_elegans		WBGENE00009663
caenorhabditis_elegans		WBGENE00219378

Paralogs (10): HDAC9 (ENSG00000048052), HDAC7 (ENSG00000061273), HDAC4 (ENSG00000068024), HDAC6 (ENSG00000094631), HDAC10 (ENSG00000100429), HDAC5 (ENSG00000108840), HDAC8 (ENSG00000147099), HDAC11 (ENSG00000163517), HDAC3 (ENSG00000171720), HDAC2 (ENSG00000196591)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:108086) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 50 distinct phenotype terms.

Mouse phenotype (MP)	Records
embryonic growth retardation	2
embryonic lethality, complete penetrance	2
decreased cell proliferation	1
abnormal hair follicle morphology	1
abnormal hair follicle orientation	1
distorted hair follicle pattern	1
abnormal zigzag hair morphology	1
alopecia	1
short hair	1
increased foot pad pigmentation	1
abnormal nail morphology	1
abnormal sebaceous gland morphology	1
abnormal epidermal layer morphology	1
thick epidermis	1
epidermal hyperplasia	1
abnormal epidermis stratum basale morphology	1
hyperkeratosis	1
decreased body size	1
short vibrissae	1
abnormal eyelid morphology	1
decreased exploration in new environment	1
abnormal coat appearance	1
abnormal allantois morphology	1
embryonic growth arrest	1
epithelioid cyst	1

+25 more (showing top 25).

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Staphylococcus aureus subsp. aureus Mu50	P64375	100.0%	Diamond
Staphylococcus aureus subsp. aureus N315	P64376	100.0%	Diamond
Pongo abelii	Q5RAG0	100.0%	Diamond
Staphylococcus aureus subsp. aureus MSSA476	Q6G8J2	100.0%	Diamond
Staphylococcus aureus subsp. aureus MW2	Q8NW34	100.0%	Diamond
Staphylococcus aureus subsp. aureus COL	Q5HF39	99.7%	Diamond
Bos taurus	Q32PJ8	99.6%	Diamond
Macaca fascicularis	Q9GKU5	99.1%	Diamond
Staphylococcus aureus subsp. aureus MRSA252	Q6GFX3	98.5%	Diamond
Xenopus tropicalis	Q28DV3	98.4%	Diamond
Xenopus laevis	Q6IRL9	98.4%	Diamond
Gallus gallus	P56519	98.2%	Diamond
Tetraodon nigroviridis	Q4SFA0	96.7%	Diamond
Oryza sativa Japonica Group	Q6YV04	95.9%	Diamond
Arabidopsis thaliana	Q8H0W2	95.5%	Diamond
Strongylocentrotus purpuratus	P56518	86.9%	Diamond
Drosophila melanogaster	Q94517	82.6%	Diamond
Zea mays	P56521	81.5%	Diamond
Pseudomonas aeruginosa PAO1	Q9I3T5	69.1%	Diamond
Dictyostelium discoideum	Q55FN5	67.1%	Diamond
Schizosaccharomyces pombe 972h-	O59702	66.6%	Diamond
Saccharomyces cerevisiae S288C	P32561	66.6%	Diamond
Bacillus subtilis subsp. subtilis str. 168	P39067	49.0%	Diamond
Burkholderia pseudomallei 1710b	Q3JUN4	43.5%	Diamond
Archaeoglobus fulgidus DSM 4304	O30107	40.8%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
FAM229A	protein-coding	100128071
MARCKSL1	protein-coding	65108
TSSK3	protein-coding	81629
BSDC1	protein-coding	55108
LCK	protein-coding	3932
FAM167B	protein-coding	84734
DCDC2B	protein-coding	149069
TMEM234	protein-coding	56063
EIF3I	protein-coding	8668

Protein

Protein identifiers

Histone deacetylase 1 — Q13547 (reviewed: Q13547)

Alternative names: Protein deacetylase HDAC1, Protein deacylase HDAC1

All UniProt accessions (5): A0ABB0MVA0, A0ABB0MVB4, Q13547, Q5TEE2, Q6IT96

UniProt curated annotations — full annotation on UniProt →

Function. Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Acts as a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin. As part of the SIN3B complex is recruited downstream of the constitutively active genes transcriptional start sites through interaction with histones and mitigates histone acetylation and RNA polymerase II progression within transcribed regions contributing to the regulation of transcription. Also functions as a deacetylase for non-histone targets, such as NR1D2, RELA, SP1, SP3, STAT3, ZNF76 and TSHZ3. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates ‘Lys-310’ in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Deacetylates NR1D2 and abrogates the effect of KAT5-mediated relieving of NR1D2 transcription repression activity. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Involved in CIART-mediated transcriptional repression of the circadian transcriptional activator: CLOCK-BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex or CRY1 through histone deacetylation. In addition to protein deacetylase activity, also has protein-lysine deacylase activity: acts as a protein decrotonylase and delactylase by mediating decrotonylation ((2E)-butenoyl) and delactylation (lactoyl) of histones, respectively.

Subunit / interactions. Part of the core histone deacetylase (HDAC) complex composed of HDAC1, HDAC2, RBBP4 and RBBP7, the core complex associates with SIN3, SAP18 and SAP30 to form the SIN3 HDAC complex. Component of the nucleosome remodeling and deacetylase (NuRD) repressor complex, composed of core proteins MTA1, MTA2, MTA3, RBBP4, RBBP7, HDAC1, HDAC2, MBD2, MBD3, and peripherally associated proteins CDK2AP1, CDK2AP2, GATAD2A, GATAD2B, CHD3, CHD4 and CHD5. The exact stoichiometry of the NuRD complex is unknown, and some subunits such as MBD2 and MBD3, GATAD2A and GATAD2B, and CHD3, CHD4 and CHD5 define mutually exclusive NuRD complexes. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Component of a mSin3A corepressor complex that contains SIN3A, SAP130, SUDS3/SAP45, ARID4B/SAP180, HDAC1 and HDAC2. Component of the SIN3B complex, which includes SIN3B, HDAC1, PHF12 and MORF4L1. Found in a trimeric complex with APBB1 and TSHZ3; the interaction between HDAC1 and APBB1 is mediated by TSHZ3. Forms a complex comprising APPL1, RUVBL2, APPL2, CTNNB1 and HDAC2. Component of a RCOR/GFI/KDM1A/HDAC complex. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2. The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A. Associates with the 9-1-1 complex; interacts with HUS1. Found in a complex with DNMT3A and HDAC7. Found in a complex with YY1, SIN3A and GON4L. Identified in a histone deacetylase complex that contains DNTTIP1, HDAC1 and MIDEAS; this complex assembles into a tetramer that contains four copies of each protein chain. Found in a complex composed of at least SINHCAF, SIN3A, HDAC1, SAP30, RBBP4, OGT and TET1. Interacts with GFI1; the interaction is direct. Interacts directly with GFI1B. Interacts with TSHZ3 (via N-terminus); the interaction is direct. Interacts with APEX1; the interaction is not dependent on the acetylated status of APEX1. Interacts with BANP. Interacts with BAZ2A/TIP5. Interacts with BCL6. Interacts with BCOR. Interacts with BHLHE40/DEC1. Interacts with BRCC3; this interaction is enhanced in the presence of PWWP2B. Interacts with BRMS1. Interacts with BRMS1L. Interacts with C10orf90/FATS (via its N-terminal); the interaction prevents binding of HDAC1 to CDKN1A/p21 and facilitates the acetylation and stabilization of CDKN1A/p21. Interacts with CBFA2T3. Interacts with CCAR2. Interacts with CDK2AP1. Interacts with CHD3. Interacts with CHD4. Interacts with CHFR. Interacts with CIART. Interacts with CDKN1A/p21. Interacts with CDK5 complexed to CDK5R1 (p25). Interacts with CRY1. Interacts with DAXX. Interacts with DDIT3/CHOP. Interacts with DDX5. Interacts with DHX36; this interaction occurs in a RNA-dependent manner. Interacts with DNMT1. Interacts with DNTTIP1. Interacts with E4F1. Interacts with EP300. Interacts with ERCC6. Interacts with GATAD2A. Interacts with HCFC1. Interacts with HDAC9. Interacts with HUS1. Interacts with INSM1. Interacts with KDM4A. Interacts with KDM5A; this interaction impairs histone deacetylation. Interacts with KDM5B. Interacts with KLF1. Interacts with MBD3L2. Interacts with MIER1. Interacts with NFE4. Interacts with NR4A2/NURR1. Interacts with NR1D2 (via C-terminus). Interacts with NRIP1. Interacts with NSD2. Interacts with PACS2. Interacts with PHB2. Interacts with PPHLN1. Interacts with PRDM6. Interacts with PRDM16. Interacts with PWWP2A in a MTA1-dependent manner. Interacts with PWWP2B. Interacts with RB1. Interacts with RERE. Interacts with SANBR (via the BTB domain). Interacts with SAMSN1. Interacts with SAP30L. Interacts with SETDB1. Interacts with SIN3A. Interacts with SMAD3. Interacts with SMAD4; positively regulated by ZBTB7A. Interacts with SMARCAD1. Interacts with SMARCA4/BRG1. Interacts with SMYD2. Interacts with SMYD4 (via MYND-type zinc finger). Interacts with SP1; the interaction deacetylates SP1 and regulates its transcriptional activity. Interacts with SP3; the interaction deacetylates SP3 and regulates its transcriptional activity. In vitro, C(18) ceramides increase this interaction and the subsequent SP3 deacetylation and SP3-mediated repression of the TERT promoter. Interacts with SPEN/MINT. Interacts with SPHK2. Interacts with SUV39H1. Interacts with TGIF. Interacts with TGIF2. Interacts with TRAF6. Interacts with TRIM28; the interaction recruits HDAC1 to E2F1 and inhibits its acetylation. Interacts with TSC22D3 isoform 1; this interaction affects HDAC1 activity on MYOG promoter and thus inhibits MYOD1 transcriptional activity. Interacts with UHRF1. Interacts with UHRF2. Interacts with ZBTB7A. Interacts with ZMYND8. Interacts with ZMYND15. Interacts with ZNF431. Interacts with ZNF516; this interaction is enhanced in the presence of PWWP2B. Interacts with ZNF541. Interacts with ZNF638. Interacts with ZNHIT1. Interacts with the non-histone region of MACROH2A1. Identified in a complex with HDAC2, KCTD19, DNTTIP1 and ZNF541. Interacts with VRK1. Interacts with SKOR2; the interaction is required for SKOR2 transcriptional repressor activity. (Microbial infection) Interacts with SV40 large T antigen.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous, with higher levels in heart, pancreas and testis, and lower levels in kidney and brain.

Post-translational modifications. Sumoylated on Lys-444 and Lys-476; which promotes enzymatic activity. Desumoylated by SENP1. Phosphorylation on Ser-421 and Ser-423 promotes enzymatic activity and interactions with NuRD and SIN3 complexes. Phosphorylated by CDK5. Ubiquitinated by CHFR, leading to its degradation by the proteasome. Ubiquitinated by KCTD11, leading to proteasomal degradation.

Activity regulation. Inositol tetraphosphate (1D-myo-inositol 1,4,5,6-tetrakisphosphate) may act as an intermolecular glue between HDAC1 and N-Cor repressor complex components.

Similarity. Belongs to the histone deacetylase family. HD type 1 subfamily.

RefSeq proteins (1): NP_004955* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000286	HDACs	Family
IPR003084	HDAC_I/II	Family
IPR023696	Ureohydrolase_dom_sf	Homologous_superfamily
IPR023801	His_deacetylse_dom	Domain
IPR037138	His_deacetylse_dom_sf	Homologous_superfamily

Pfam: PF00850

Enzyme classification (BRENDA)

• EC 3.5.1.98 — histone deacetylase (BRENDA: 33 organisms, 161 substrates, 590 inhibitors, 88 Km, 32 kcat entries)

Substrate kinetics (BRENDA)

32 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
FLUOR DE LYS HDAC8 SUBSTRATE	0.14–1.1	9
AC-KHK(ACETYL)K(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.273–2.403	6
FLUOR DE LYS HDAC SUBSTRATE	0.013–0.088	6
AC-FEK(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.0023–0.0359	5
AC-GGK(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.0043–0.0877	5
AC-GS(PO3)K(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.0123–0.0666	5
AC-GSK(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.004–0.0241	5
AC-IHK(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.0007–0.108	5
AC-KYK(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.0044–0.107	4
FLUOR DE LYS	—	4
AC-LYK(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.0069–0.03	3
AC-VLK(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.0119–0.0221	3
RHK(ACETYL)K(ACETYL)-FLUOROPHORE	0.16–1.1	3
AC-DQK(ACETYL)-7-AMIDO-4-METHYLCOUMARIN	0.0024–0.0165	2
BENZYLOXYCARBONYL-L-LYS(ACETYL)-7-AMIDO-4-METHYL	0.078–0.099	2

Catalyzed reactions (Rhea)

• N(6)-acetyl-L-lysyl-[protein] + H2O = L-lysyl-[protein] + acetate (RHEA:58108)
• N(6)-acetyl-L-lysyl-[histone] + H2O = L-lysyl-[histone] + acetate (RHEA:58196)
• N(6)-(2E)-butenoyl-L-lysyl-[protein] + H2O = (2E)-2-butenoate + L-lysyl-[protein] (RHEA:69172)
• N(6)-[(S)-lactoyl]-L-lysyl-[protein] + H2O = (S)-lactate + L-lysyl-[protein] (RHEA:81387)

UniProt features (86 total): helix 19, mutagenesis site 13, strand 12, modified residue 10, cross-link 10, turn 7, binding site 6, compositionally biased region 4, region of interest 2, chain 1, sequence conflict 1, active site 1

Structure

Experimental structures (PDB)

12 structures by resolution:

PDB	Title	Method	Resolution (Å)
7SME	p107 pocket domain complexed with HDAC1 peptide	X-RAY DIFFRACTION	2.64
9R4I	An auto inhibitory loop in the MiDAC histone deacetylase complex	ELECTRON MICROSCOPY	2.92
4BKX	The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD …	X-RAY DIFFRACTION	3
5ICN	HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on …	X-RAY DIFFRACTION	3.3
8VPQ	The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML	ELECTRON MICROSCOPY	3.3
8VRT	The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant	ELECTRON MICROSCOPY	3.42
8VOJ	The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and …	ELECTRON MICROSCOPY	3.77
6Z2J	The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex	ELECTRON MICROSCOPY	4
6Z2K	The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex	ELECTRON MICROSCOPY	4.5
7AO8	Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex	ELECTRON MICROSCOPY	4.5
7AO9	Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex	ELECTRON MICROSCOPY	6.1
7AOA	Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex	ELECTRON MICROSCOPY	19.4

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13547-F1	86.41	0.76

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Hydrolases, Predicted intracellular proteins, Plasma proteins, FDA approved drug targets, Small molecule drugs

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH enhanced · IF enhanced

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1)

Position	Role
141

Ligand- & substrate-binding residues (6)

Position	Role
176	Zn(2+)
178	Zn(2+)
264	Zn(2+)
270	1D-myo-inositol 1,4,5,6-tetrakisphosphate
27	1D-myo-inositol 1,4,5,6-tetrakisphosphate
31	1D-myo-inositol 1,4,5,6-tetrakisphosphate

Post-translational modifications (20)

Type	Positions
N6-acetyllysine	74, 220
S-nitrosocysteine	261, 273
Phosphoserine	393, 406, 409, 421, 423
N6-methylated lysine	432
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)	74, 438, 444, 456, 457, 473, 476, 480
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo)	444, 476

Mutagenesis-validated functional residues (13)

Position	Phenotype
136–138	impaired protein deacetylase activity without affecting the protein decrotonylase activity.
141	abolishes histone deacetylase and decrotonylase activities.
287	abolishes interaction with chfr; when associated with i-297.
297	abolishes interaction with chfr; when associated with y-287.
391–482	strongly decreases deacetylase activity, and disrupts interaction with nurd and sin3 complexes.
421	strongly decreases deacetylase activity, and disrupts interaction with nurd and sin3 complexes.
421	slightly decreases deacetylase activity.
423	strongly decreases deacetylase activity, and disrupts interaction with nurd and sin3 complexes.
423	decreases deacetylase activity.
424–426	abolished histone deacetylase and decrotonylase activities.
424	slightly decreases deacetylase activity, no effect on interaction with nurd and sin3 complexes.
425	no effect on deacetylase activity, no effect on interaction with nurd and sin3 complexes.
426	decreases deacetylase activity, and disrupts interaction with nurd and sin3 complexes.

Function

Pathways and Gene Ontology

Reactome pathways

26 curated (TAS) of 112; 19 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

showing 60 of 112 pathways:

ID	Pathway	Evidence
R-HSA-2894862	Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants ⚕	curated
R-HSA-2644606	Constitutive Signaling by NOTCH1 PEST Domain Mutants ⚕	curated
R-HSA-9022538	Loss of MECP2 binding ability to 5mC-DNA ⚕	curated
R-HSA-9725371	Nuclear events stimulated by ALK signaling in cancer ⚕	curated
R-HSA-9679191	Potential therapeutics for SARS ⚕	curated
R-HSA-3769402	Deactivation of the beta-catenin transactivating complex	curated
R-HSA-2173795	Downregulation of SMAD2/3:SMAD4 transcriptional activity	curated
R-HSA-9018519	Estrogen-dependent gene expression	curated
R-HSA-983231	Factors involved in megakaryocyte development and platelet production	curated
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex	curated
R-HSA-1538133	G0 and Early G1	curated
R-HSA-3214815	HDACs deacetylate histones	curated
R-HSA-9940951	Interaction of NuRD complexes with transcription factors	curated
R-HSA-9764725	Negative Regulation of CDH1 Gene Transcription	curated
R-HSA-350054	Notch-HLH transcription pathway	curated
R-HSA-9937850	NuRD complex assembly	curated
R-HSA-73762	RNA Polymerase I Transcription Initiation	curated
R-HSA-8936459	RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function	curated
R-HSA-9022692	Regulation of MECP2 expression and activity	curated
R-HSA-9824594	Regulation of MITF-M-dependent genes involved in apoptosis	curated
R-HSA-9825892	Regulation of MITF-M-dependent genes involved in cell cycle and proliferation	curated
R-HSA-6804758	Regulation of TP53 Activity through Acetylation	curated
R-HSA-2173796	SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription	curated
R-HSA-9701898	STAT3 nuclear events downstream of ALK signaling	curated
R-HSA-4551638	SUMOylation of chromatin organization proteins	curated
R-HSA-9856649	Transcriptional and post-translational regulation of MITF-M expression and activity	curated
R-HSA-1643685	Disease ⚕	—
R-HSA-5663202	Diseases of signal transduction by growth factor receptors and second messengers ⚕	—
R-HSA-9675151	Disorders of Developmental Biology ⚕	—
R-HSA-9697154	Disorders of Nervous System Development ⚕	—
R-HSA-5663205	Infectious disease ⚕	—
R-HSA-9005891	Loss of function of MECP2 in Rett syndrome ⚕	—
R-HSA-9005895	Pervasive developmental disorders ⚕	—
R-HSA-9679506	SARS-CoV Infections ⚕	—
R-HSA-9725370	Signaling by ALK fusions and activated point mutants ⚕	—
R-HSA-9700206	Signaling by ALK in cancer ⚕	—
R-HSA-2894858	Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer ⚕	—
R-HSA-2644602	Signaling by NOTCH1 PEST Domain Mutants in Cancer ⚕	—
R-HSA-2644603	Signaling by NOTCH1 in Cancer ⚕	—
R-HSA-9824446	Viral Infection Pathways ⚕	—
R-HSA-418990	Adherens junctions interactions	—
R-HSA-9843745	Adipogenesis	—
R-HSA-1640170	Cell Cycle	—
R-HSA-69278	Cell Cycle, Mitotic	—
R-HSA-446728	Cell junction organization	—
R-HSA-1500931	Cell-Cell communication	—
R-HSA-421270	Cell-cell junction organization	—
R-HSA-3247509	Chromatin modifying enzymes	—
R-HSA-4839726	Chromatin organization	—
R-HSA-73887	Death Receptor Signaling	—
R-HSA-195253	Degradation of beta-catenin by the destruction complex	—
R-HSA-1266738	Developmental Biology	—
R-HSA-9976102	Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)	electronic
R-HSA-427389	ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression	electronic
R-HSA-8939211	ESR-mediated signaling	—
R-HSA-212165	Epigenetic regulation of gene expression	—
R-HSA-9614085	FOXO-mediated transcription	—
R-HSA-9615017	FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes	electronic
R-HSA-69206	G1/S Transition	—
R-HSA-69205	G1/S-Specific Transcription	electronic

MSigDB gene sets: 632 (showing top): GOBP_CIRCADIAN_RHYTHM, PID_HDAC_CLASSI_PATHWAY, REACTOME_SIGNALING_BY_NOTCH, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_EPITHELIUM_DEVELOPMENT, REACTOME_G1_S_SPECIFIC_TRANSCRIPTION, REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX, MORF_SMC1L1, PID_TELOMERASE_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_STRIATED_MUSCLE_CELL_DIFFERENTIATION, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_NEGATIVE_REGULATION_OF_MUSCLE_CELL_DIFFERENTIATION, GOBP_EMBRYONIC_DIGIT_MORPHOGENESIS, REACTOME_RNA_POLYMERASE_I_TRANSCRIPTION_INITIATION, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION

GO Biological Process (37): negative regulation of transcription by RNA polymerase II (GO:0000122), chromatin organization (GO:0006325), chromatin remodeling (GO:0006338), DNA methylation-dependent constitutive heterochromatin formation (GO:0006346), DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of cell population proliferation (GO:0008284), epidermal cell differentiation (GO:0009913), positive regulation of gene expression (GO:0010628), negative regulation of gene expression (GO:0010629), negative regulation of cell migration (GO:0030336), negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512), heterochromatin formation (GO:0031507), circadian regulation of gene expression (GO:0032922), positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148), cellular response to platelet-derived growth factor stimulus (GO:0036120), odontogenesis of dentin-containing tooth (GO:0042475), regulation of cell fate specification (GO:0042659), embryonic digit morphogenesis (GO:0042733), negative regulation of apoptotic process (GO:0043066), host-mediated suppression of viral transcription (GO:0043922), negative regulation of gene expression, epigenetic (GO:0045814), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of embryonic development (GO:0045995), positive regulation of smooth muscle cell proliferation (GO:0048661), negative regulation of androgen receptor signaling pathway (GO:0060766), hair follicle placode formation (GO:0060789), eyelid development in camera-type eye (GO:0061029), fungiform papilla formation (GO:0061198), negative regulation of canonical Wnt signaling pathway (GO:0090090), negative regulation of stem cell population maintenance (GO:1902455), positive regulation of stem cell population maintenance (GO:1902459), regulation of stem cell differentiation (GO:2000736), circadian rhythm (GO:0007623), rhythmic process (GO:0048511)

GO Molecular Function (28): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979), core promoter sequence-specific DNA binding (GO:0001046), transcription corepressor binding (GO:0001222), p53 binding (GO:0002039), transcription corepressor activity (GO:0003714), histone deacetylase activity (GO:0004407), enzyme binding (GO:0019899), protein lysine deacetylase activity (GO:0033558), Krueppel-associated box domain binding (GO:0035851), histone deacetylase binding (GO:0042826), metal ion binding (GO:0046872), NF-kappaB binding (GO:0051059), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), E-box binding (GO:0070888), DNA-binding transcription factor binding (GO:0140297), histone deacetylase activity, hydrolytic mechanism (GO:0141221), histone decrotonylase activity (GO:0160009), protein lysine delactylase activity (GO:0160216), promoter-specific chromatin binding (GO:1990841), transcription cis-regulatory region binding (GO:0000976), DNA binding (GO:0003677), chromatin binding (GO:0003682), protein binding (GO:0005515), hydrolase activity (GO:0016787), hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides (GO:0016811), nucleosomal DNA binding (GO:0031492), protein decrotonylase activity (GO:0160008)

GO Cellular Component (14): histone deacetylase complex (GO:0000118), chromatin (GO:0000785), heterochromatin (GO:0000792), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), NuRD complex (GO:0016581), transcription repressor complex (GO:0017053), protein-containing complex (GO:0032991), neuronal cell body (GO:0043025), Sin3-type complex (GO:0070822), ribonucleoprotein complex (GO:1990904), transcription regulator complex (GO:0005667)

Reactome top-level categories

17 top-level categories:

Category	Pathways
G0 and Early G1	2
TCF dependent signaling in response to WNT	2
Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer	2
Mitotic G1 phase and G1/S transition	1
p75 NTR receptor-mediated signalling	1
Signaling by NOTCH1	1
Signaling by NOTCH1 PEST Domain Mutants in Cancer	1
Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer	1
Chromatin modifying enzymes	1
Generic Transcription Pathway	1
Positive epigenetic regulation of rRNA expression	1
Negative epigenetic regulation of rRNA expression	1
SUMO E3 ligases SUMOylate target proteins	1
Degradation of beta-catenin by the destruction complex	1
Regulation of TP53 Activity	1
G1/S Transition	1
RNA Polymerase I Transcription	1

GO top-level categories

showing 60 of 82 GO namespaces:

Category	Terms
cellular anatomical structure	4
gene expression	3
regulation of gene expression	3
transcription by RNA polymerase II	2
negative regulation of DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
protein binding	2
histone modifying activity	2
catalytic activity, acting on a protein	2
chromatin	2
histone deacetylase complex	2
transcription regulator complex	2
protein-containing complex	2
regulation of transcription by RNA polymerase II	1
cellular component organization	1
chromatin organization	1
constitutive heterochromatin formation	1
RNA biosynthetic process	1
regulation of DNA-templated transcription	1
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
epidermis development	1
epithelial cell differentiation	1
positive regulation of macromolecule biosynthetic process	1
negative regulation of macromolecule biosynthetic process	1
cell migration	1
regulation of cell migration	1
negative regulation of cell motility	1
transforming growth factor beta receptor signaling pathway	1
regulation of transforming growth factor beta receptor signaling pathway	1
negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	1
cellular component assembly	1
heterochromatin boundary formation	1
negative regulation of gene expression, epigenetic	1
heterochromatin organization	1
circadian rhythm	1
estrogen receptor signaling pathway	1
positive regulation of intracellular steroid hormone receptor signaling pathway	1
regulation of intracellular estrogen receptor signaling pathway	1
response to platelet-derived growth factor	1
cellular response to growth factor stimulus	1
odontogenesis	1
cell fate specification	1
regulation of cell fate commitment	1
embryonic limb morphogenesis	1
embryonic morphogenesis	1
apoptotic process	1
regulation of apoptotic process	1
negative regulation of programmed cell death	1
cis-regulatory region sequence-specific DNA binding	1
core promoter sequence-specific DNA binding	1
transcription cis-regulatory region binding	1
transcription coregulator binding	1
transcription coregulator activity	1
protein lysine deacetylase activity	1
deacetylase activity	1
protein domain specific binding	1
enzyme binding	1
cation binding	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 38 of 79 annotations. The rest are phylogenetic / computational / electronic (IEA).

38 experimentally-supported GO terms:

GO term	NS	Evidence
DNA methylation-dependent constitutive heterochromatin formation	BP	genetic interaction
chromatin organization	BP	direct assay
chromatin remodeling	BP	direct assay
host-mediated suppression of viral transcription	BP	mutant phenotype
negative regulation of DNA-templated transcription	BP	mutant phenotype
negative regulation of androgen receptor signaling pathway	BP	direct assay
negative regulation of canonical Wnt signaling pathway	BP	genetic interaction
negative regulation of gene expression	BP	mutant phenotype
negative regulation of gene expression, epigenetic	BP	mutant phenotype
negative regulation of transcription by RNA polymerase II	BP	direct assay
positive regulation of DNA-templated transcription	BP	direct assay
positive regulation of cell population proliferation	BP	mutant phenotype
positive regulation of intracellular estrogen receptor signaling pathway	BP	mutant phenotype
positive regulation of transcription by RNA polymerase II	BP	direct assay
regulation of transcription by RNA polymerase II	BP	genetic interaction
NuRD complex	CC	direct assay
Sin3-type complex	CC	direct assay
chromatin	CC	direct assay
cytosol	CC	direct assay
histone deacetylase complex	CC	direct assay
nucleoplasm	CC	direct assay
nucleus	CC	direct assay
protein-containing complex	CC	direct assay
DNA-binding transcription factor binding	MF	physical interaction
NF-kappaB binding	MF	physical interaction
RNA polymerase II cis-regulatory region sequence-specific DNA binding	MF	genetic interaction
RNA polymerase II core promoter sequence-specific DNA binding	MF	direct assay
RNA polymerase II-specific DNA-binding transcription factor binding	MF	physical interaction
core promoter sequence-specific DNA binding	MF	direct assay
enzyme binding	MF	physical interaction
histone deacetylase activity	MF	direct assay
histone deacetylase binding	MF	physical interaction
histone decrotonylase activity	MF	direct assay
p53 binding	MF	physical interaction
protein lysine deacetylase activity	MF	direct assay
protein lysine delactylase activity	MF	direct assay
transcription corepressor activity	MF	direct assay
transcription corepressor binding	MF	physical interaction

Protein interactions and networks

STRING

showing 15 of 5,872 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HDAC1	SAP30	O75446	923
HDAC1	H3-3A	P06351	886
HDAC1	RCOR1	Q9UKL0	886
HDAC1	H3C14	Q71DI3	886
HDAC1	H3-5	Q6NXT2	886
HDAC1	H3C1	P02295	886
HDAC1	H3-4	Q16695	886
HDAC1	H3-7	Q5TEC6	886
HDAC1	SIN3A	Q96ST3	885
HDAC1	KDM1A	O60341	880
HDAC1	RBBP4	P31149	877
HDAC1	DNMT1	P26358	874
HDAC1	SIRT1	Q96EB6	872
HDAC1	KAT2B	Q92831	856
HDAC1	HDAC2	Q92769	850

IntAct

Human interaction partners of HDAC1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 132 partners by confidence:

Partner	Interaction type	MIscore	Records
RB1	association	0.960	16
HDAC2	physical association	0.950	5
MTA2	physical association	0.950	5
RCOR1	physical association	0.950	4
MTA1	physical association	0.940	3
MIER1	direct interaction	0.930	5
CHD4	colocalization	0.930	2
SIN3A	physical association	0.930	1
RBBP4	association	0.920	2
RBBP7	physical association	0.920	1
KDM1A	association	0.910	7
MBD3	physical association	0.910	1
MTA3	association	0.880	2
ZNF516	physical association	0.880	2
DNTTIP1	association	0.880	1
ARID5B	colocalization	0.870	3
SINHCAF	colocalization	0.870	3
CHD3	colocalization	0.850	1
CDK2AP1	association	0.840	3
EHMT2	association	0.840	3
BRMS1	physical association	0.830	3
PWWP2A	colocalization	0.830	3
C16orf87	physical association	0.820	2
TNRC18	association	0.790	1
TRERF1	association	0.790	1
TP53	physical association	0.770	6
CSNK2A1	phosphorylation reaction	0.760	1
ZNF609	association	0.730	1
ZBTB16	physical association	0.700	6
BCL11B	physical association	0.700	2

BioGRID (2,945 interactions; top human partners by supporting records in a sample of 600 records): HDAC2 (Affinity Capture-Western; 15 records), SIN3A (Affinity Capture-Western; 15 records), CHD4 (Affinity Capture-Western; 10 records), RBBP4 (Co-fractionation; 10 records), KDM1A (Co-fractionation; 9 records), MTA1 (Co-fractionation; 9 records), PML (Affinity Capture-Western; 8 records), RBBP7 (Affinity Capture-MS; 8 records), MTA2 (Co-fractionation; 7 records), RB1 (Reconstituted Complex; 7 records), TP53 (Affinity Capture-Western; 7 records), HMG20B (Affinity Capture-MS; 6 records), CDYL (Affinity Capture-MS; 5 records), FOXK2 (Affinity Capture-Western; 5 records), MBD2 (Affinity Capture-Western; 5 records)

SIGNOR signaling

showing 58 of 82 signaling interactions:

A	Effect	B	Mechanism
CSNK2A1	up-regulates	HDAC1	phosphorylation
HDAC1	down-regulates	MYOD1	binding
BCL3	up-regulates	HDAC1	binding
HDAC1	up-regulates	CCND1	binding
HDAC1	“down-regulates quantity by repression”	CEBPA	“transcriptional regulation”
PPARG	down-regulates	HDAC1	relocalization
HDAC1	down-regulates	RELA	binding
DDX5	up-regulates	HDAC1	binding
“N-[4-[(hydroxyamino)-oxomethyl]phenyl]carbamic acid [6-(diethylaminomethyl)-2-naphthalenyl]methyl ester”	down-regulates	HDAC1	“chemical inhibition”
CUDC-907	down-regulates	HDAC1	“chemical inhibition”
entinostat	down-regulates	HDAC1	“chemical inhibition”
N-hydroxy-2-[4-[[(1-methyl-3-indolyl)methylamino]methyl]-1-piperidinyl]-5-pyrimidinecarboxamide	down-regulates	HDAC1	“chemical inhibition”
N-(2-aminophenyl)-4-[[[4-(3-pyridinyl)-2-pyrimidinyl]amino]methyl]benzamide	down-regulates	HDAC1	“chemical inhibition”
E2F1	up-regulates	HDAC1	binding
HDAC1	“form complex”	SMAD7/HDAC1/E2F-1	binding
HDAC3	up-regulates	HDAC1	binding
3-[(dimethylamino)methyl]-N-[2-[4-[(hydroxyamino)-oxomethyl]phenoxy]ethyl]-2-benzofurancarboxamide	down-regulates	HDAC1	“chemical inhibition”
HDAC1	up-regulates	FLI1	deacetylation
HDAC1	down-regulates	CEBPA	“transcriptional regulation”
HDAC1	down-regulates	NfKb-p65/p50	binding
HDAC1	“form complex”	“CoREST-HDAC complex”	binding
TFAP4	“up-regulates activity”	HDAC1	binding
SMARCAD1	“up-regulates activity”	HDAC1	binding
CSNK2A2	“up-regulates activity”	HDAC1	phosphorylation
NKX3-1	“down-regulates activity”	HDAC1	binding
BCOR	“up-regulates activity”	HDAC1	binding
HDAC1	“down-regulates quantity by repression”	DNMT1	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	ESR1	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	CLDN7	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	ABCB1	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	FSHR	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	HSPA5	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	SNAI2	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	EGR1	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	GAD1	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	RELN	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	UBE2D3	“transcriptional regulation”
HDAC1	“down-regulates quantity by repression”	VDR	“transcriptional regulation”
NUP98-HOXA9	“up-regulates activity”	HDAC1	binding
(S)-N-Hydroxy-4-(3-methyl-2-phenylbutanamido)benzamide	“down-regulates activity”	HDAC1	“chemical inhibition”
HDAC1	“form complex”	“MBD2/NuRD complex”	binding
HDAC1	“form complex”	“MBD3/NuRD complex”	binding
HDAC1	“form complex”	“BHC complex”	binding
TSHZ3	“up-regulates activity”	HDAC1	relocalization
HDAC1	“form complex”	Sin3B_complex	binding
HDAC1	“form complex”	“MECP2/SIN3A/HDAC complex”	binding
HDAC1	“down-regulates quantity by repression”	SERPINB5	“transcriptional regulation”
PYHIN1	“down-regulates quantity by repression”	HDAC1	“transcriptional regulation”
CHFR	“down-regulates quantity by destabilization”	HDAC1	polyubiquitination
MDM2	“down-regulates quantity by destabilization”	HDAC1	ubiquitination
PBK	“up-regulates activity”	HDAC1	phosphorylation
ABL1	“up-regulates activity”	HDAC1	phosphorylation
HDAC1	“down-regulates quantity”	HES1	“transcriptional regulation”
HDAC1	“up-regulates activity”	FOXO	deacetylation
HDAC1	“up-regulates activity”	FOXO3	deacetylation
NR3C1	up-regulates	HDAC1	binding
HDAC1	“up-regulates activity”	GLI1	deacetylation
HDAC1	“down-regulates quantity by repression”	KLK3	“transcriptional regulation”

Protein complexes (CORUM) (84)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

showing 60 of 84 complexes by size:

Complex	Subunits	Members
★ ALL-1 supercomplex	28	MTA2, SIN3A, SMARCC2, TAF12, TBP, WDR5, EFTUD2, RBBP7, SAP18, SYMPK, TAF9, HDAC1, KMT2A, MBD3, RBBP5, SAP30, SMARCA2, TAF1, TAF6, CPSF2, HDAC2, KDM1A, RAN, RBBP4, SMARCA5, SMARCB1, SMARCC1, CHD3
★ Emerin complex 32	22	HDAC1, RBL2, SMARCC1, SMARCC2, TBL1Y, BANF2, DPY30, HDAC3, H3C1, LMNB1, MED4, RBL1, SAP18, TRIM28, ACTB, CHD4, EMD, NMI, RCOR1, SMARCB1, SPTAN1, TBL1XR1
★ LARC complex (LCR-associated remodeling complex)	19	SMARCC1, SMARCC2, SMARCD2, SMARCE1, ACTL6A, CHD4, MBD3, RBBP4, ACTB, MTA2, SMARCA4, HDAC1, HDAC2, HNRNPC, MBD2, ARID1A, DPF2, GATAD2B, SMARCB1
★ HCF-1 complex	18	HSPA8, RBBP7, SAP30, SETD1A, SIN3A, HCFC1, OGT, SP1, WDR5, HDAC1, SIN3B, SUDS3, ASH2L, HSP90AA1, RBBP4, HDAC2, HSPA4, HSPA5
★ Anti-HDAC2 complex	17	CHD3, CHD4, GTF2I, HDAC2, HMG20B, PHF21A, RBBP4, ZMYM2, ZMYM3, GSE1, HDAC1, MTA1, MTA2, RCOR1, SIN3A, KDM1A, RBBP7
★ CtBP complex	17	ZEB1, CBX4, CDYL, CTBP1, HDAC1, HDAC2, RCOR1, ZEB2, EHMT2, KDM1A, RCOR3, RREB1, ZNF516, CTBP2, LCOR, EHMT1, ZNF217
★ SNF2h-cohesin-NuRD complex	16	MBD2, MTA2, RBBP7, SMARCA5, MTA1, RBBP4, HDAC2, RAD21, SMC3, STAG1, STAG2, BAZ1A, HDAC1, MBD3, SMC1A, CHD3
★ SIN3-ING1b complex II	16	ARID1A, ING1, RBBP7, ACTL6A, ARID4B, RBBP4, SAP18, SAP30, SMARCA4, SMARCC1, HDAC1, HDAC2, SMARCD1, SIN3A, SMARCB1, SMARCC2
★ BRM-SIN3A complex	15	RBBP4, SMARCA2, SMARCB1, SMARCC2, SMARCD1, ACTL6A, HDAC1, HDAC2, PRMT5, SIN3A, SMARCD3, ARID1A, SMARCC1, SMARCD2, SMARCE1
★ LSD1 complex	14	PHF21B, RCOR1, RREB1, ZMYM2, CTBP1, HDAC1, HMG20A, HSPA1A, KDM1A, RCOR3, ZNF217, HMG20B, HSPA1B, PHF21A
★ ING2 complex	13	BRMS1L, SAP30, SIN3A, SUDS3, ARID4A, BRMS1, HDAC1, HDAC2, ING2, RBBP4, RBBP7, SAP130, ARID4B
★ MBD3-NuRD complex	13	HDAC2, MBD3, RBBP4, ZNF598, CDK2AP1, CHD3, CHD4, GATAD2B, HDAC1, MTA2, RBBP7, ZMYND8, GATAD2A
★ PRC1.6a complex	13	RYBP, TFDP1, HDAC1, MAX, MGA, PCGF6, WDR5, CBX3, E2F6, HDAC2, L3MBTL2, RING1, RNF2
★ PRC1.6b complex	13	CBX3, HDAC1, L3MBTL2, MGA, PCGF6, RING1, WDR5, E2F6, HDAC2, MAX, RNF2, TFDP1, YAF2
★ anti-BHC110 complex	11	GSE1, HDAC2, ZMYM2, ZMYM3, ZNF217, GTF2I, HDAC1, HMG20B, KDM1A, PHF21A, RCOR1
★ SIN3-SAP25 complex	11	HDAC2, RBBP4, SAP30, SIN3A, SUDS3, RBBP7, SAP130, SAP18, SAP25, ARID4B, HDAC1
★ BHC110 complex	10	ZNF217, GSE1, HDAC1, KDM1A, PHF21A, RCOR1, ZMYM2, ZNF516, HDAC2, HMG20B
★ Emerin regulatory complex	9	BANF1, EMD, H3C1, LMO7, ACTB, H1-1, HDAC1, HDAC3, RBL1
★ mSin3A corepressor complex	9	ARID4B, HDAC2, RBBP4, RBBP7, SAP130, SUDS3, HDAC1, SAP30, SIN3A
★ CtBP core complex	9	EHMT2, HDAC1, HDAC2, RCOR1, ZEB1, CTBP1, EHMT1, KDM1A, CTBP2
★ HDAC1-associated protein complex	9	HDAC1, KDM1A, MBD2, MBD3, MTA2, RBBP4, RBBP7, RCOR1, CHD3
★ HDAC1-associated core complex cII	9	CHD3, HDAC1, MBD2, MTA2, RBBP4, RBBP7, RCOR1, GATAD2A, MBD3
★ MeCP1 complex	9	MTA2, RBBP4, RBBP7, MBD3, CHD4, GATAD2B, HDAC1, HDAC2, MBD2
★ SIN3-ING1b complex I	9	SAP18, SAP30, ARID4B, HDAC1, RBBP4, SIN3A, HDAC2, ING1, RBBP7
★ CDYL-complex	9	HDAC1, MIER1, REST, WIZ, CDYL, EHMT1, EHMT2, HDAC2, SETDB1
★ SIX3-LSD1-NuRD(MTA3) complex	9	HDAC1, HDAC2, KDM1A, MBD2, RBBP7, MBD3, MTA3, RBBP4, SIX3
★ SAP complex (Sin3-associated protein complex)	8	SAP30, SIN3A, ARID4B, HDAC1, HDAC2, RBBP4, RBBP7, SAP130
★ MeCP1 complex	8	RBBP7, CHD4, HDAC1, HDAC2, MBD2, MBD3, MTA2, RBBP4
★ BRMS1-mSin3A corepressor complex	8	SAP30, SIN3A, SIN3B, BRMS1, HDAC1, HDAC2, RBBP4, RBBP7
★ MTA2 complex	8	MBD3, MTA2, RBBP4, RBBP7, SIN3A, CHD4, HDAC1, HDAC2
★ NCOR2 complex	7	NCOR2, SAP30, SIN3A, HDAC1, HDAC2, HDAC3, NCOR1
★ SIN3 complex	7	SAP30, SIN3A, HDAC1, HDAC2, RBBP4, RBBP7, SAP18
★ DNMT3B complex	7	HDAC1, KIF4A, SIN3A, SMARCA5, SMC2, SMC4, DNMT3B
★ NuRD.1 complex	7	CHD4, HDAC1, HDAC2, MBD3, MTA1, RBBP4, RBBP7
★ Mi2/NuRD complex	7	MBD3, MTA2, RBBP4, RBBP7, CHD4, HDAC1, HDAC2
★ NRD complex (Nucleosome remodeling and deacetylation complex)	7	HDAC2, KDM1A, MTA1, RBBP4, CHD3, CHD4, HDAC1
★ CoREST-HDAC complex	7	HMG20B, KDM1A, PHF21A, RCOR1, ZNF217, HDAC1, HDAC2
★ SIN3-HDAC-SAP30-ARID4 complex	7	RBBP4, RBBP7, SAP30, SIN3A, ARID4B, HDAC1, HDAC2
★ BRAF35-BRCA2 complex	7	KDM1A, PHF21A, RCOR1, BRCA2, HDAC1, HDAC2, HMG20B
★ NK-3-Groucho-HIPK2-SIN3A-RbpA48-HDAC1 complex	6	NKX3-1, RBBP4, SIN3A, TLE1, HDAC1, HIPK2
★ NCOR-SIN3-HDAC-HESX1 complex	6	HESX1, NCOR2, SIN3A, SIN3B, HDAC1, HDAC2
★ RBL2 complex (DNMT1, E2F4, E2F5, HDAC1, RBL2, SUV39H1)	6	DNMT1, E2F4, E2F5, HDAC1, RBL2, SUV39H1
★ RBL2 complex (EP300, E2F4, E2F5, HDAC1, RBL2, SUV39H1)	6	E2F4, E2F5, EP300, HDAC1, RBL2, SUV39H1
★ BHC complex	6	HMG20B, KDM1A, PHF21A, RCOR1, HDAC1, HDAC2
★ SMAR1-HDAC1-SIN3A-SIN3B-p107-p130 repressor complex	6	BANP, HDAC1, RBL1, RBL2, SIN3A, SIN3B
★ DNMT1-associated protein complex	6	USP7, DNMT1, HDAC1, KAT5, PCNA, UHRF1
★ MTA1 complex	6	HDAC1, HDAC2, MBD3, MTA1, RBBP4, RBBP7
★ PID complex	5	CHD4, HDAC1, MBD3, MTA2, RBBP4
★ mSin3A corepressor complex	5	RBBP7, SIN3A, HDAC1, HDAC2, RBBP4
★ SMAD2-SMAD4-FAST1-TGIF-HDAC1 complex, TGF(beta) induced	5	FOXH1, HDAC1, SMAD2, SMAD4, TGIF1
★ SWI/SNF-related chromatin-remodeling complex	5	MECP2, SIN3A, SMARCA2, SMARCE1, HDAC1
★ BAZ2A-DNMT1-DNMT3B-HDAC1-SMARCA5 complex	5	DNMT1, DNMT3B, HDAC1, SMARCA5, BAZ2A
★ Mi2/NuRD-BCL6-MTA3 complex	5	BCL6, CHD4, HDAC1, MBD3, MTA3
★ XFIM complex	5	GTF2I, HDAC1, HDAC2, KDM1A, ZMYM3
★ CREBBP-EP300-HDAC1-SP1-SP3 complex	5	CREBBP, EP300, HDAC1, SP1, SP3
★ MTA1-HDAC core complex	5	HDAC1, HDAC2, MTA1, RBBP4, RBBP7
★ PARP3-EZH2-HDAC1-SUZ12-YY1 complex	5	HDAC1, PARP3, SUZ12, YY1, EZH2
★ DNMT1-EHMT2-HDAC1-UHRF1 complex	4	DNMT1, EHMT2, HDAC1, UHRF1
★ DNMT1-E2F1-HDAC1-RB1 complex	4	DNMT1, E2F1, HDAC1, RB1
★ SKI-NCOR1-SIN3A-HDAC1 complex	4	HDAC1, NCOR1, SIN3A, SKI

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 132 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Regulation of TP53 Activity through Acetylation	9	43.7×	2e-11
Transcriptional regulation of brown and beige adipocyte differentiation by EBF2	10	40.5×	3e-12
Regulation of endogenous retroelements	8	31.4×	5e-09
Regulation of PTEN gene transcription	16	30.4×	3e-17
RNA Polymerase I Transcription Initiation	10	23.8×	5e-10
HDACs deacetylate histones	17	21.7×	5e-16
SUMOylation of transcription cofactors	8	20.7×	1e-07
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)	13	20.2×	5e-12

GO biological processes:

GO term	Partners	Fold	FDR
regulation of stem cell differentiation	9	57.9×	3e-12
negative regulation of gene expression via chromosomal CpG island methylation	5	44.2×	6e-06
negative regulation of stem cell population maintenance	6	38.6×	8e-07
DNA methylation-dependent constitutive heterochromatin formation	7	32.0×	2e-07
positive regulation of miRNA transcription	12	29.3×	1e-12
positive regulation of stem cell population maintenance	8	23.1×	2e-07
negative regulation of Notch signaling pathway	5	18.2×	4e-04
embryonic digit morphogenesis	7	17.7×	1e-05

Disease & clinical

Genetic variants

Variant evidence for HDAC1: 63 ClinVar records (1 pathogenic / likely pathogenic); 1 PharmGKB clinical annotation. Per-variant detail is on Sugi Variant.

ClinVar

63 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	31
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
208751	NM_004964.3(HDAC1):c.461A>G (p.Asn154Ser)	Likely pathogenic	criteria provided, single submitter	1

Per-variant reference — Sugi Variant

Explore HDAC1’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 20 predictions of 1,143):

Position(s)	Effect	Δscore	Sites
1:32292197	donor_gain	1.0000
1:32292219–32292220	donor_loss	1.0000	3
1:32316655	acceptor_gain	1.0000
1:32316663–32316664	acceptor_loss	1.0000	6
1:32316783–32316784	donor_loss	1.0000	4
1:32324477	acceptor_gain	1.0000
1:32326932	acceptor_gain	1.0000
1:32327036	donor_gain	1.0000
1:32327637	donor_gain	1.0000
1:32327647	donor_gain	1.0000

AlphaMissense

2,185 missense substitutions predicted likely pathogenic (of 3,217 scored), across 404 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M30	9	0.992	1.000
M350	9	0.973	0.997
M37	9	0.969	1.000
M194	9	0.921	1.000
D99	8	1.000	1.000
H140	8	1.000	1.000
H141	8	1.000	1.000
D174	8	1.000	1.000
D176	8	1.000	1.000
H178	8	1.000	1.000
H179	8	1.000	1.000
D181	8	1.000	1.000
H199	8	1.000	1.000
D264	8	1.000	1.000
D269	8	1.000	1.000
H28	8	0.999	1.000
H68	8	0.999	1.000
F150	8	0.999	1.000
D155	8	0.999	1.000
F205	8	0.999	1.000

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	2.99e-10

Disease associations

OMIM: gene MIM:601241 | disease phenotypes:

GenCC curated gene-disease

1 curated gene-disease records:

Disease	Classification	Inheritance	Records
congenital heart disease	Disputed Evidence	Autosomal dominant

ClinGen Gene-Disease Validity

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

1 validity classifications:

Disease	Classification	Inheritance
congenital heart disease	Disputed	AD

Mondo (1): congenital heart disease (MONDO:0005453)

MeSH disease descriptors

1 disease descriptors:

Descriptor	Name	Tree numbers
D006330	Heart Defects, Congenital	C14.240.400; C14.280.400; C16.131.240.400

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (17): CHEMBL2093865 (PROTEIN FAMILY), CHEMBL2111429 (PROTEIN FAMILY), CHEMBL3038483 (PROTEIN FAMILY), CHEMBL325 (SINGLE PROTEIN), CHEMBL3430896 (PROTEIN FAMILY), CHEMBL3430897 (PROTEIN FAMILY), CHEMBL3885589 (PROTEIN FAMILY), CHEMBL3885590 (PROTEIN COMPLEX), CHEMBL4106143 (PROTEIN COMPLEX), CHEMBL4106187 (PROTEIN FAMILY)

Drugs by curated mechanism of action (ChEMBL)

Drugs whose curated ChEMBL mechanism of action targets the HDAC1 protein itself — single-protein targets only (drugs acting on a protein family or complex that merely includes it are excluded). Includes antibodies and oligonucleotides that bioactivity screening does not capture.

2 curated-mechanism drugs:

Drug	Modality	Max phase
VORINOSTAT	Small molecule	4
MOCETINOSTAT	Small molecule	2

Molecules with ChEMBL bioactivity

Phase ≥1, by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 871,097 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

48 molecules by phase:

Molecule	Name	Phase	Patents
CHEMBL98	VORINOSTAT	4	51,304
CHEMBL1487	ATORVASTATIN	4	69,270
CHEMBL408513	BELINOSTAT	4	8,184
CHEMBL487253	BENDAMUSTINE	4	31,460
CHEMBL325041	BORTEZOMIB	4	13,415
CHEMBL118	CELECOXIB	4	113,751
CHEMBL178	DAUNORUBICIN	4	205,873
CHEMBL329522	EXIFONE	4	1,557
CHEMBL1213492	GIVINOSTAT	4	2,960
CHEMBL503	LOVASTATIN	4	93,071
CHEMBL1078178	MOMELOTINIB	4	3,649
CHEMBL483254	PANOBINOSTAT	4	12,172
CHEMBL1469	PHENYLBUTANOIC ACID	4	37,412
CHEMBL343448	ROMIDEPSIN	4	13,626
CHEMBL1746	SODIUM PHENYLBUTYRATE	4	5,678
CHEMBL109	VALPROIC ACID	4	66,702
CHEMBL2103863	ABEXINOSTAT	3	2,290
CHEMBL145	CAFFEIC ACID	3	36,727
CHEMBL140	CURCUMIN	3	95,185
CHEMBL27759	ENTINOSTAT	3	6,811
CHEMBL1851943	PRACINOSTAT	3
CHEMBL235191	TACEDINALINE	3
CHEMBL3621988	TUCIDINOSTAT	3
CHEMBL272980	MOCETINOSTAT	2
CHEMBL191482	AR-42	2
CHEMBL8260	BAICALEIN	2
CHEMBL14227	BUTYRIC ACID	2
CHEMBL284616	CHLOROGENIC ACID	2
CHEMBL3693786	CITARINOSTAT	2
CHEMBL356066	DACINOSTAT	2
CHEMBL4283683	DOMATINOSTAT	2
CHEMBL3622533	FIMEPINOSTAT	2
CHEMBL1232461	MOLIBRESIB	2
CHEMBL1801250	NANATINOSTAT	2
CHEMBL504369	NICOXAMAT	2
CHEMBL2105763	QUISINOSTAT	2
CHEMBL4296717	RESMINOSTAT	2
CHEMBL2364628	RICOLINOSTAT	2
CHEMBL62381	SODIUM BUTYRATE	2
CHEMBL3989941	TINOSTAMUSTINE	2
CHEMBL3287255	BISTHIANOSTAT	1
CHEMBL5314582	BOCODEPSIN BESYLATE	1
CHEMBL598797	CUDC-101	1
CHEMBL96	GAMMA-AMINOBUTYRIC ACID	1
CHEMBL3126832	OBP-801	1
CHEMBL353581	PYROXAMIDE	1
CHEMBL609583	R-306465	1
CHEMBL99	TRICHOSTATIN	1

PharmGKB: 1 entry (CPIC guideline: no)

PharmGKB clinical annotations

1 annotations by evidence level (1 strongest → 4):

Variant	Association	Level	Drugs	Phenotypes
rs1741981	Efficacy	3	corticosteroids	Asthma

PharmGKB variants

1 variants:

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1741981	HDAC1	3	3.25	1	corticosteroids

PharmGKB variant annotations

Per-publication pharmacogenomic findings for this gene (significant associations).

2 published findings:

Variant	Drug(s)	Category	Finding	PMID
rs1741981	Corticosteroids For Systemic Use	Efficacy	Genotype CC is associated with decreased response to Corticosteroids For Systemic Use in people with Asthma as compared to genotypes CT + TT.	PMID:24307847
rs1741981	corticosteroids	Efficacy	Genotype CC is associated with decreased response to corticosteroids in children with Asthma as compared to genotypes CT + TT.	PMID:24307847

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Histone deacetylases (HDACs)

Most potent curated ligand interactions (36 total), top 25:

Ligand	Action	Affinity	Parameter
romidepsin	Inhibition	11.82	pKi
apicidin	Inhibition	10.4	pKi
quisinostat	Inhibition	9.96	pIC50
compound 25ap [PMID: 37796543]	Inhibition	9.92	pIC50
trichostatin A	Inhibition	9.7	pKi
martinostat	Inhibition	9.52	pIC50
dacinostat	Inhibition	9.26	pKi
vorinostat	Inhibition	8.89	pKi
scriptaid	Inhibition	8.82	pKi
fimepinostat	Inhibition	8.77	pIC50
panobinostat	Inhibition	8.52	pEC50
CHR-3996	Inhibition	8.52	pIC50
CUDC-101	Inhibition	8.35	pIC50
abexinostat	Inhibition	8.15	pIC50
mocetinostat	Inhibition	8.05	pKi
givinostat	Inhibition	7.55	pEC50
RGFP109	Inhibition	7.49	pKi
citarinostat	Inhibition	7.46	pIC50
belinostat	Inhibition	7.39	pEC50
resminostat	Inhibition	7.37	pIC50
pracinostat	Inhibition	7.31	pIC50
ricolinostat	Inhibition	7.24	pIC50
ACY-738	Inhibition	7.03	pIC50
BML-281	Inhibition	7.0	pIC50
suprastat	Inhibition	6.93	pIC50

Binding affinities (BindingDB)

4923 measured of 6030 human assays (6100 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
GNF-Pf-1011	IC50	0.001 nM
(E)-3-[3-[[ethyl(2-ethylbutyl)amino]methyl]-2-methylimidazo[1,2-a]pyridin-7-yl]-N-hydroxyprop-2-enamide	IC50	0.01 nM	US-8648092: Imidazo[1,2-a]pyridine derivatives: preparation and pharmaceutical applications
(E)-3-[2-butyl-3-(butylaminomethyl)imidazo[1,2-a]pyridin-7-yl]-N-hydroxyprop-2-enamide	IC50	0.02 nM	US-8648092: Imidazo[1,2-a]pyridine derivatives: preparation and pharmaceutical applications
CHEMBL114184	IC50	0.02 nM
(E)-3-[2-butyl-3-[[butyl(ethyl)amino]methyl]imidazo[1,2-a]pyridin-7-yl]-N-hydroxyprop-2-enamide	IC50	0.06 nM	US-8648092: Imidazo[1,2-a]pyridine derivatives: preparation and pharmaceutical applications
CHEMBL432618	IC50	0.062 nM
CHEMBL321689	IC50	0.082 nM
JNJ-26481585	IC50	0.1 nM
CHEMBL432243	IC50	0.109 nM
CHEMBL113303	IC50	0.11 nM
CHEMBL3622726	IC50	0.12 nM
CHEMBL3930620	IC50	0.12 nM
CHEMBL3936651	IC50	0.13 nM
(E)-N-hydroxy-3-[4-[[2-(1-methylindol-3-yl)ethylamino]methyl]phenyl]prop-2-enamide	IC50	0.2 nM	US-10188756: Imaging histone deacetylases with a radiotracer using positron emission tomography
CHEMBL3317812	IC50	0.2 nM
CHEMBL1793991	IC50	0.2 nM
CHEMBL2047701	IC50	0.2 nM
CHEMBL3126833	IC50	0.2 nM
CHEMBL3317811	IC50	0.21 nM
CHEMBL3929484	IC50	0.27 nM
CHEMBL1836142	IC50	0.28 nM
CHEMBL3317810	IC50	0.29 nM
(E)-3-[4-[[1-adamantylmethyl(methyl)amino]methyl]phenyl]-N-hydroxyprop-2-enamide	IC50	0.3 nM	US-10188756: Imaging histone deacetylases with a radiotracer using positron emission tomography
CHEMBL3329621	IC50	0.3 nM
Largazole Thiol	IC50	0.4 nM
CHEMBL2158745	IC50	0.4 nM
CHEMBL3593247	IC50	0.4 nM
CHEMBL3329622	IC50	0.4 nM
6-((9S,13aR)-5-(S)-1-Benzyl-8,8-dimethyl-4,7,10,13-tetraoxo-tetradecahydro-3a,6,9,12-tetraaza-cyclopentacyclododecen-11-yl)-hexanoic acid hydroxyamide	IC50	0.4 nM
HC toxin	KI	0.44 nM
CHEMBL4214018	IC50	0.44 nM
CHEMBL3828518	IC50	0.45 nM
8-[4-amino-3-[4-[(2-fluoro-5-methylphenyl)carbamoylamino]phenyl]pyrazolo[3,4-d]pyrimidin-1-yl]-N-hydroxyoctanamide	IC50	0.47 nM	US-9695181: Hydroximic acid derivatives and medical applications therof
CHEMBL2047694	IC50	0.48 nM
CHEMBL3828636	IC50	0.49 nM
CHEMBL4209174	IC50	0.54 nM
CHEMBL3828492	IC50	0.55 nM
CHEMBL3827517	IC50	0.55 nM
CHEMBL99392	KI	0.6 nM
CHEMBL3759059	IC50	0.6 nM
CHEMBL2047702	IC50	0.6 nM
CHEMBL2408777	KI	0.62 nM
CHEMBL3317818	IC50	0.62 nM
CHEMBL4207111	IC50	0.63 nM
CHEMBL3827814	IC50	0.65 nM
CHEMBL3920583	IC50	0.65 nM
CHEMBL3957055	IC50	0.69 nM
CHEMBL3759921	IC50	0.7 nM
(6S,9S,12S,14aR)-6-((S)-sec-Butyl)-9-(1-methoxy-1H-indol-3-ylmethyl)-12-(6-oxo-octyl)-decahydro-4a,7,10,13-tetraaza-benzocyclododecene-5,8,11,14-tetraone	IC50	0.7 nM
CHEMBL4204833	IC50	0.71 nM

ChEMBL bioactivities

6100 potent at pChembl≥5 of 6100 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
10.70	IC50	0.02	nM	CHEMBL114184
10.52	Ki	0.03	nM	QUISINOSTAT
10.40	Ki	0.04	nM	APICIDIN
10.30	IC50	0.05	nM	CHEMBL4861467
10.25	Ki	0.056	nM	CHEMBL4250302
10.24	Ki	0.057	nM	CHEMBL4239232
10.21	IC50	0.062	nM	CHEMBL432618
10.20	Ki	0.063	nM	CHEMBL4237636
10.12	Ki	0.075	nM	CHEMBL4237803
10.10	IC50	0.08	nM	CHEMBL4641682
10.09	IC50	0.082	nM	CHEMBL321689
10.09	IC50	0.082	nM	CHEMBL6133082
10.07	IC50	0.085	nM	CHEMBL4649205
10.01	Ki	0.097	nM	CHEMBL4251203
10.00	IC50	0.1	nM	CHEMBL4641682
10.00	IC50	0.1	nM	QUISINOSTAT
9.98	IC50	0.105	nM	CHEMBL6145619
9.96	IC50	0.109	nM	CHEMBL432243
9.96	IC50	0.11	nM	CHEMBL113303
9.96	IC50	0.11	nM	QUISINOSTAT
9.96	IC50	0.11	nM	CHEMBL4568666
9.96	IC50	0.11	nM	CHEMBL4644038
9.96	IC50	0.11	nM	CHEMBL4876610
9.96	IC50	0.11	nM	CHEMBL4878197
9.96	IC50	0.11	nM	TRAPOXIN B
9.94	IC50	0.116	nM	CHEMBL6169315
9.92	IC50	0.12	nM	FR-135313
9.90	IC50	0.125	nM	CHEMBL6174035
9.85	IC50	0.142	nM	CHEMBL5618643
9.82	Ki	0.15	nM	CHEMBL4246561
9.82	IC50	0.15	nM	CHEMBL4438063
9.82	IC50	0.15	nM	TRICHOSTATIN
9.80	IC50	0.16	nM	CHEMBL4637689
9.80	IC50	0.16	nM	DOMATINOSTAT
9.77	IC50	0.17	nM	CHEMBL4862152
9.77	IC50	0.17	nM	CHEMBL5433552
9.72	IC50	0.19	nM	CHEMBL4532398
9.72	IC50	0.19	nM	CHEMBL4642518
9.70	IC50	0.2	nM	CHEMBL2047701
9.70	IC50	0.2	nM	ROMIDEPSIN
9.70	IC50	0.2	nM	CHEMBL3126833
9.70	IC50	0.2	nM	CHEMBL3317812
9.70	Ki	0.2	nM	TRICHOSTATIN
9.70	IC50	0.2	nM	CHEMBL2371007
9.70	IC50	0.2	nM	CHEMBL4634501
9.70	IC50	0.2	nM	CHEMBL4746782
9.70	IC50	0.2	nM	CHEMBL4780309
9.70	IC50	0.2	nM	ENTINOSTAT
9.70	IC50	0.2	nM	CHEMBL4860000
9.70	IC50	0.2	nM	CHEMBL5288006

PubChem BioAssay actives

3192 with measured affinity, of 6100 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
N-hydroxy-2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]pyrimidine-5-carboxamide	1236442: Inhibition of human HDAC1	ki	<0.0001	uM
N-hydroxy-2-[4-(4-methylphenyl)sulfonylpiperazin-1-yl]-1,3-thiazole-5-carboxamide	1941741: Inhibition of HDAC (unknown origin)	ic50	0.0001	uM
1-[5-(hydroxyamino)-5-oxopentyl]-N-(4-methyl-1,3-thiazol-2-yl)-4-oxoquinoline-3-carboxamide	1794854: HDAC Activity screening from Article 10.3109/14756366.2013.827675: “Quinolone-based HDAC inhibitors.”	ic50	0.0001	uM
N-hydroxy-6-[[2-(4-methylanilino)-3,4-dioxocyclobuten-1-yl]amino]heptanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0001	uM
(6R)-6-[[3,4-dioxo-2-[[2-(trifluoromethyl)-1H-indol-6-yl]amino]cyclobuten-1-yl]amino]-N-hydroxyheptanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0001	uM
N-hydroxy-6-[[2-(4-methoxyanilino)-3,4-dioxocyclobuten-1-yl]amino]hexanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0001	uM
N-hydroxy-6-[[2-(4-methylanilino)-3,4-dioxocyclobuten-1-yl]amino]hexanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0001	uM
N-hydroxy-6-[[2-(4-methoxyanilino)-3,4-dioxocyclobuten-1-yl]amino]-6-methylheptanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0001	uM
N-hydroxy-5-[1-[[2-(4-methoxyanilino)-3,4-dioxocyclobuten-1-yl]amino]cyclobutyl]pentanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0001	uM
N-[(1S)-1-[5-(2-fluorophenyl)-1H-imidazol-2-yl]-7-(1,2-oxazol-3-yl)-7-oxoheptyl]-1-methylazetidine-3-carboxamide	1664940: Inhibition of full length human recombinant FLAG-tagged HDAC1 expressed in HEK293F cells using FLUOR DE LYS as substrate preincubated for 3 hrs followed by substrate addition and measured after 60 mins by fluorescence based assay	ic50	0.0001	uM
(2S)-6-(cyclopropylmethyl)-N-[(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]-7-oxononyl]-6-azaspiro[2.5]octane-2-carboxamide	1662500: Inhibition of HDAC1 (unknown origin)	ic50	0.0001	uM
(2S)-N-[(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]-7-oxononyl]-6-propan-2-yl-6-azaspiro[2.5]octane-2-carboxamide	1662500: Inhibition of HDAC1 (unknown origin)	ic50	0.0001	uM
(3S,6S)-6-(6-oxooctyl)-21-oxa-5,8,18,25,32-pentazahexacyclo[23.2.2.17,10.111,15.114,18.01,3]dotriaconta-7,9,11(31),12,14,16-hexaene-4,30-dione	1754652: Inhibition of HDAC1 (unknown origin)	ic50	0.0001	uM
(3S,6S)-12-methoxy-6-(6-oxooctyl)-5,8,18,27,34-pentazahexacyclo[25.2.2.17,10.111,15.114,18.01,3]tetratriaconta-7,9,11,13,15(33),16-hexaene-4,32-dione	1754652: Inhibition of HDAC1 (unknown origin)	ic50	0.0001	uM
(3S,9S,12R)-3-benzyl-6,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-1,4,7,10-tetrazabicyclo[10.3.0]pentadecane-2,5,11-trione	1622972: Inhibition of HDAC1 (unknown origin)	ic50	0.0001	uM
(5R,8S,11S)-8-(1H-imidazol-5-ylmethyl)-5-methyl-11-[(E)-4-sulfanylbut-1-enyl]-10-oxa-3,17-dithia-7,14,19,20-tetrazatricyclo[14.2.1.12,5]icosa-1(18),2(20),16(19)-triene-6,9,13-trione	1185952: Inhibition of HDAC1 (unknown origin) incubated at 37 degC for 30 mins	ic50	0.0002	uM
(5R,8S,11S)-8-[(4-hydroxyphenyl)methyl]-5-methyl-11-[(E)-4-sulfanylbut-1-enyl]-10-oxa-3,17-dithia-7,14,19,20-tetrazatricyclo[14.2.1.12,5]icosa-1(18),2(20),16(19)-triene-6,9,13-trione	1185952: Inhibition of HDAC1 (unknown origin) incubated at 37 degC for 30 mins	ic50	0.0002	uM
(2R)-N-[4-[1-[7-(hydroxyamino)-7-oxoheptyl]-4-morpholin-4-ylpyrazolo[5,4-d]pyrimidin-6-yl]phenyl]-2-methylmorpholine-4-carboxamide	1614126: Inhibition of recombinant full length HDAC1 (unknown origin) using Ac-peptide-AMC as substrate preincubated for 15 mins followed by substrate addition and measured after 1 hr by fluorescence assay	ic50	0.0002	uM
6-[[3,4-dioxo-2-[4-(trifluoromethyl)anilino]cyclobuten-1-yl]amino]-N-hydroxyhexanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0002	uM
N-[(1S)-1-[5-(2-fluorophenyl)-1,3-oxazol-2-yl]-7-(1,2-oxazol-3-yl)-7-oxoheptyl]-1-methylazetidine-3-carboxamide	1664940: Inhibition of full length human recombinant FLAG-tagged HDAC1 expressed in HEK293F cells using FLUOR DE LYS as substrate preincubated for 3 hrs followed by substrate addition and measured after 60 mins by fluorescence based assay	ic50	0.0002	uM
(2S)-N-[(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]-7-oxononyl]-6-methyl-6-azaspiro[2.5]octane-2-carboxamide	1662500: Inhibition of HDAC1 (unknown origin)	ic50	0.0002	uM
(3S,6S)-6-(6-oxooctyl)-5,8,18,27,34-pentazahexacyclo[25.2.2.17,10.111,15.114,18.01,3]tetratriaconta-7,9,11(33),12,14,16-hexaene-4,32-dione	1754652: Inhibition of HDAC1 (unknown origin)	ic50	0.0002	uM
(5R,8S,11S)-8-benzyl-5-methyl-11-[(E)-4-sulfanylbut-1-enyl]-10-oxa-3,17-dithia-7,14,19,20-tetrazatricyclo[14.2.1.12,5]icosa-1(18),2(20),16(19)-triene-6,9,13-trione	1185952: Inhibition of HDAC1 (unknown origin) incubated at 37 degC for 30 mins	ic50	0.0003	uM
(5R,8S,11S)-5-methyl-11-[(E)-4-[[(E)-4-[(5R,8S,11S)-5-methyl-6,9,13-trioxo-8-propan-2-yl-10-oxa-3,17-dithia-7,14,19,20-tetrazatricyclo[14.2.1.12,5]icosa-1(18),2(20),16(19)-trien-11-yl]but-3-enyl]disulfanyl]but-1-enyl]-8-propan-2-yl-10-oxa-3,17-dithia-7,14,19,20-tetrazatricyclo[14.2.1.12,5]icosa-1(18),2(20),16(19)-triene-6,9,13-trione	1188977: Inhibition of HDAC1 (unknown origin) incubated for 30 mins in presence of BSA and DTT by fluorescence assay	ic50	0.0003	uM
6-[[3,4-dioxo-2-[4-(trifluoromethyl)anilino]cyclobuten-1-yl]amino]-N-hydroxy-6-methylheptanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0003	uM
6-[[3,4-dioxo-2-[4-(trifluoromethyl)anilino]cyclobuten-1-yl]amino]-N-hydroxyheptanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0003	uM
N-hydroxy-6-[[2-(4-methoxyanilino)-3,4-dioxocyclobuten-1-yl]amino]heptanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0003	uM
6-[(2-anilino-3,4-dioxocyclobuten-1-yl)amino]-N-hydroxyhexanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0003	uM
N-hydroxy-6-[[2-[(2-methyl-1H-indol-6-yl)amino]-3,4-dioxocyclobuten-1-yl]amino]hexanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0003	uM
(2S)-6-ethyl-N-[(1S)-1-[5-(7-methoxy-2-methylquinolin-6-yl)-1H-imidazol-2-yl]-7-oxononyl]-6-azaspiro[2.5]octane-2-carboxamide	1916027: Inhibition of recombinant human HDAC1 using BML-KI104 as substrate preincubated for 3 hrs followed by substrate addition measured after 60 mins by modified FLUOR DE LYS assay	ic50	0.0003	uM
(2S)-6-methyl-N-[(1S)-1-[5-(2-methyl-1-oxoisoquinolin-6-yl)-1H-imidazol-2-yl]-7-oxononyl]-6-azaspiro[2.5]octane-2-carboxamide	1754652: Inhibition of HDAC1 (unknown origin)	ic50	0.0003	uM
(2S)-6-cyclobutyl-N-[(1S)-1-[5-(7-methoxy-2-methylquinolin-6-yl)-1H-imidazol-2-yl]-7-oxononyl]-6-azaspiro[2.5]octane-2-carboxamide	1916027: Inhibition of recombinant human HDAC1 using BML-KI104 as substrate preincubated for 3 hrs followed by substrate addition measured after 60 mins by modified FLUOR DE LYS assay	ic50	0.0003	uM
(2S)-N-[(1S)-1-[5-(7-ethyl-2-methylquinolin-6-yl)-1H-imidazol-2-yl]-7-oxononyl]-6-methyl-6-azaspiro[2.5]octane-2-carboxamide	1916027: Inhibition of recombinant human HDAC1 using BML-KI104 as substrate preincubated for 3 hrs followed by substrate addition measured after 60 mins by modified FLUOR DE LYS assay	ic50	0.0003	uM
(2S)-N-[(1S)-1-[5-(7-methoxy-2-methylquinolin-6-yl)-1,3-oxazol-2-yl]-7-oxononyl]-6-methyl-6-azaspiro[2.5]octane-2-carboxamide	1916027: Inhibition of recombinant human HDAC1 using BML-KI104 as substrate preincubated for 3 hrs followed by substrate addition measured after 60 mins by modified FLUOR DE LYS assay	ic50	0.0003	uM
(3S,6S)-6-(6-oxooctyl)-22-oxa-5,8,18,26,33-pentazahexacyclo[24.2.2.17,10.111,15.114,18.01,3]tritriaconta-7,9,11(32),12,14,16-hexaene-4,31-dione	1754652: Inhibition of HDAC1 (unknown origin)	ic50	0.0003	uM
tert-butyl (2R)-2-[(2-methylpropan-2-yl)oxycarbonylamino]-3-[[(E)-4-[(5R,8S,11S)-5-methyl-6,9,13-trioxo-8-propan-2-yl-10-oxa-3,17-dithia-7,14,19,20-tetrazatricyclo[14.2.1.12,5]icosa-1(18),2(20),16(19)-trien-11-yl]but-3-enyl]disulfanyl]propanoate	1188977: Inhibition of HDAC1 (unknown origin) incubated for 30 mins in presence of BSA and DTT by fluorescence assay	ic50	0.0004	uM
N-hydroxy-2-[[2-(4-methoxyphenyl)-9-methyl-6-morpholin-4-ylpurin-8-yl]methyl-methylamino]pyrimidine-5-carboxamide	1312847: Inhibition of full length C-terminal His/FLAG-tagged human recombinant HDAC1 expressed in baculovirus infected insect Sf9 cells using Ac-peptide-AMC as substrate assessed as release of AMC preincubated for 15 mins followed by substrate addition measured after 1 hr by fluorescence assay	ic50	0.0004	uM
(3S,6R,9S,12R)-6,9-dimethyl-3-[6-[(2S)-oxiran-2-yl]-6-oxohexyl]-1,4,7,10-tetrazabicyclo[10.3.0]pentadecane-2,5,8,11-tetrone	1972856: Binding affinity to HDAC1 (unknown origin) assessed as inhibition constant(ki,1)	ki	0.0004	uM
N-hydroxy-6-[[2-(3-methylanilino)-3,4-dioxocyclobuten-1-yl]amino]hexanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0004	uM
7-[2-(4-fluoro-3-hydroxyphenyl)-6-morpholin-4-ylpurin-9-yl]-N-hydroxyheptanamide	1702055: Inhibition of HDAC1 in human HeLa nuclear extract using Boc-Lys(Ac)-AMC as substrate measured after 2 hrs by fluorescence based assay	ic50	0.0005	uM
N-hydroxy-2-[methyl-[(9-methyl-6-morpholin-4-yl-2-pyridin-3-ylpurin-8-yl)methyl]amino]pyrimidine-5-carboxamide	1312847: Inhibition of full length C-terminal His/FLAG-tagged human recombinant HDAC1 expressed in baculovirus infected insect Sf9 cells using Ac-peptide-AMC as substrate assessed as release of AMC preincubated for 15 mins followed by substrate addition measured after 1 hr by fluorescence assay	ic50	0.0005	uM
7-cyclopentyl-2-[4-[[6-(hydroxyamino)-6-oxohexyl]carbamoyl]anilino]-N,N-dimethylpyrrolo[2,3-d]pyrimidine-6-carboxamide	1469380: Inhibition of HDAC1 (unknown origin)	ic50	0.0005	uM
6-[[3,4-dioxo-2-[4-(trifluoromethyl)anilino]cyclobuten-1-yl]amino]-N-hydroxyoctanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0005	uM
6-[[2-[4-(dimethylamino)-3-methoxyanilino]-3,4-dioxocyclobuten-1-yl]amino]-N-hydroxyhexanamide	1399812: Inhibition of human recombinant HDAC1 using Fluor de Lys as substrate after 2 hrs by fluorescence method	ki	0.0005	uM
(5R,8S,11S)-11-[(Z)-2-fluoro-4-sulfanylbut-1-enyl]-5-methyl-8-propan-2-yl-10-oxa-3,17-dithia-7,14,19,20-tetrazatricyclo[14.2.1.12,5]icosa-1(18),2(20),16(19)-triene-6,9,13-trione	1566037: Inhibition of recombinant full length C-terminal FLAG/His-tagged human HDAC1 expressed in baculovirus infected Sf9 cells using Ac-peptide-AMC as substrate preincubated for 15 mins followed by substrate addition and measured after 60 mins by fluorescence based assay	ic50	0.0005	uM
4-[9-[7-(hydroxyamino)-7-oxoheptyl]-6-morpholin-4-ylpurin-2-yl]benzamide	1702055: Inhibition of HDAC1 in human HeLa nuclear extract using Boc-Lys(Ac)-AMC as substrate measured after 2 hrs by fluorescence based assay	ic50	0.0006	uM
tert-butyl 4-[[(5R,8S,11S)-5-methyl-6,9,13-trioxo-11-[(E)-4-sulfanylbut-1-enyl]-10-oxa-3,17-dithia-7,14,19,20-tetrazatricyclo[14.2.1.12,5]icosa-1(18),2(20),16(19)-trien-8-yl]methyl]imidazole-1-carboxylate	1185952: Inhibition of HDAC1 (unknown origin) incubated at 37 degC for 30 mins	ic50	0.0006	uM
N-hydroxy-2-[[2-(3-hydroxyphenyl)-9-methyl-6-morpholin-4-ylpurin-8-yl]methyl-methylamino]pyrimidine-5-carboxamide	1312847: Inhibition of full length C-terminal His/FLAG-tagged human recombinant HDAC1 expressed in baculovirus infected insect Sf9 cells using Ac-peptide-AMC as substrate assessed as release of AMC preincubated for 15 mins followed by substrate addition measured after 1 hr by fluorescence assay	ic50	0.0006	uM
2-[[2-(4-aminophenyl)-9-methyl-6-morpholin-4-ylpurin-8-yl]methyl-methylamino]-N-hydroxypyrimidine-5-carboxamide	1312847: Inhibition of full length C-terminal His/FLAG-tagged human recombinant HDAC1 expressed in baculovirus infected insect Sf9 cells using Ac-peptide-AMC as substrate assessed as release of AMC preincubated for 15 mins followed by substrate addition measured after 1 hr by fluorescence assay	ic50	0.0006	uM
N-hydroxy-2-[methyl-[(9-methyl-6-morpholin-4-yl-2-pyridin-4-ylpurin-8-yl)methyl]amino]pyrimidine-5-carboxamide	1312847: Inhibition of full length C-terminal His/FLAG-tagged human recombinant HDAC1 expressed in baculovirus infected insect Sf9 cells using Ac-peptide-AMC as substrate assessed as release of AMC preincubated for 15 mins followed by substrate addition measured after 1 hr by fluorescence assay	ic50	0.0006	uM

CTD chemical–gene interactions

102 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, decreases expression, decreases reaction, increases expression, decreases activity (+3 more)	8
trichostatin A	decreases expression, decreases reaction, increases expression, decreases activity	6
Estradiol	decreases expression, affects cotreatment, decreases reaction, increases expression, affects binding (+1 more)	5
sodium arsenite	affects expression, decreases reaction, increases expression, decreases expression	4
Curcumin	affects localization, decreases reaction, decreases expression	4
Resveratrol	increases reaction, affects binding, decreases reaction, increases acetylation, increases activity (+1 more)	3
Decitabine	affects binding, decreases reaction	3
Arsenic Trioxide	affects cotreatment, increases reaction, decreases expression, increases phosphorylation, affects binding	3
Vorinostat	decreases reaction, increases expression, decreases activity, decreases expression	3
bisphenol A	affects expression, affects splicing	2
hydroquinone	increases expression, decreases reaction	2
benzyloxycarbonylleucyl-leucyl-leucine aldehyde	affects localization, decreases reaction, decreases expression, increases degradation	2
Doxorubicin	affects binding, increases reaction, decreases expression	2
Hydrogen Peroxide	decreases expression, increases expression	2
Tetrachlorodibenzodioxin	affects binding, increases reaction, affects cotreatment, decreases reaction, increases expression	2
Theophylline	increases activity, increases expression	2
Cyclosporine	decreases expression	2
Genistein	decreases expression, decreases reaction, affects binding, increases reaction	2
Butyric Acid	affects binding, decreases reaction, increases expression	2
Particulate Matter	decreases reaction, increases degradation, increases expression, decreases expression, increases abundance	2
FR900359	affects phosphorylation	1
napabucasin	decreases expression	1
TAK-243	decreases sumoylation	1
2,4,6-tribromophenol	increases expression	1
honokiol	affects binding, decreases activity	1
benzo(b)fluoranthene	decreases expression	1
chlamydocin	decreases activity	1
2,2’-methylenebis(4-methyl-6-tert-butylphenol)	affects expression, affects response to substance	1
withaferin A	decreases expression	1
decabromobiphenyl ether	increases expression	1

ChEMBL screening assays

3675 unique, capped per target: 3604 binding, 57 admet, 13 functional, 1 toxicity

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1003756	Binding	Inhibition of HDAC in human NB4 cells assessed as induction of histone H3 acetylation after 6 hrs by Western blot analysis	Design, synthesis and preliminary biological evaluation of new hydroxamate histone deacetylase inhibitors as potential antileukemic agents. — *Bioorg Med Chem Lett*
CHEMBL4346553	ADMET	Inhibition of HDAC in HUVEC using Boc-Lys(Ac)-AMC as substrate preincubated for 12 hrs followed by substrate addition and measured after 4 hrs by fluorimetry	Discovery of Novel Fungal Lanosterol 14α-Demethylase (CYP51)/Histone Deacetylase Dual Inhibitors to Treat Azole-Resistant Candidiasis. — *J Med Chem*
CHEMBL5049470	Functional	In vivo inhibition of HDAC in HEL cells xenografted in BALB/C mouse assessed as upregulation of caspase-9 levels at 5 to 10 mg/kg by immunohistochemical staining method	Evodiamine-Inspired Topoisomerase-Histone Deacetylase Dual Inhibitors: Novel Orally Active Antitumor Agents for Leukemia Therapy. — *J Med Chem*

Cellosaurus cell lines

15 cell lines: 11 cancer cell line, 3 embryonic stem cell, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A2L7	SEES3-1V human HDAC1, clone1	Embryonic stem cell	Male
CVCL_A2L8	SEES3-1V human HDAC1, clone2	Embryonic stem cell	Male
CVCL_A2L9	SEES3-1V human HDAC1, clone3	Embryonic stem cell	Male
CVCL_B8H6	Abcam HCT 116 HDAC1 KO	Cancer cell line	Male
CVCL_B8WJ	Abcam MCF-7 HDAC1 KO	Cancer cell line	Female
CVCL_B9JG	Abcam A-549 HDAC1 KO	Cancer cell line	Male
CVCL_D7R4	Ubigene A-549 HDAC1 KO	Cancer cell line	Male
CVCL_D8MA	Ubigene HCT 116 HDAC1 KO	Cancer cell line	Male
CVCL_D9G3	Ubigene HEK293 HDAC1 KO	Transformed cell line	Female
CVCL_E0E6	Ubigene HeLa HDAC1 KO	Cancer cell line	Female

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 300 trials:

NCT	Phase	Status	Title
NCT00668824	Phase 4	UNKNOWN	Improved Diagnosis of Congenital Heart Disease by Magnetic Resonance Imaging Using Vasovist
NCT01368705	Phase 4	COMPLETED	Nitrogen Balance in Infants After Post Cardiothoracic Surgery
NCT01619982	Phase 4	COMPLETED	Pre-operative Prophylaxis With Vancomycin and Cefazolin in Pediatric Cardiovascular Surgery Patients
NCT02122679	Phase 4	WITHDRAWN	Tranexamic Acid Effect on Platelet Aggregation Following Infant Cardiopulmonary Bypass
NCT02527811	Phase 4	UNKNOWN	Ulinastatin Injection in in Pediatric Patients Undergoing Open Heart Surgery
NCT03014700	Phase 4	COMPLETED	Fibrinogen Concentrate vs Cryoprecipitate
NCT03408340	Phase 4	TERMINATED	Paravertebral Nerve Blocks in Neonates
NCT03630796	Phase 4	UNKNOWN	Effect of Sevoflurane in Postoperative Troponin I Levels in Children Undergoing Congenital Heart Defects Surgery
NCT03667703	Phase 4	COMPLETED	Stress Ulcer Prophylaxis Versus Placebo in Critically Ill Infants With Congenital Heart Disease
NCT04453761	Phase 4	UNKNOWN	Thiamine Influenced on Substrate Energy Effectiveness in Indonesian Children Undergoing Cardiopulmonary Bypass
NCT06668389	Phase 4	RECRUITING	Sodium-Glucose Cotransporter 2 Inhibitors for Repaired Tetralogy of Fallot Patients for Enhancement of Cardio-Pulmonary Status Trial
NCT07499154	Phase 4	NOT_YET_RECRUITING	Perioperative Lidocaine for Lung Protection in Infants Undergoing Cardiac Surgery
NCT00000470	Phase 3	COMPLETED	Infant Heart Surgery: Central Nervous System Sequelae of Circulatory Arrest
NCT00000494	Phase 3	COMPLETED	Management of Patent Ductus in Premature Infants
NCT01134302	Phase 3	UNKNOWN	Hybrid Versus Norwood Management Strategies in Infants Undergoing Single Ventricle Palliation
NCT01607983	Phase 3	WITHDRAWN	Effects of Pulmonary Vasodilation Upon VA Coupling in Fontan Patients
NCT01662011	Phase 3	UNKNOWN	Application of Neurally Adjusted Ventilatory Assist to Children After Congenital Cardiac Surgery
NCT02320669	Phase 3	COMPLETED	Phase 3 Triiodothyronine Supplementation for Infants After Cardiopulmonary Bypass
NCT02615262	Phase 3	COMPLETED	Intraoperative Dexamethasone in Pediatric Cardiac Surgery
NCT03153137	Phase 3	COMPLETED	Clinical Study Assessing the Efficacy and Safety of Macitentan in Fontan-palliated Subjects
NCT03154476	Phase 3	COMPLETED	Role of Sildenafil for Fontan Associated Liver Disease (SiFALD) Study
NCT04536194	Phase 3	COMPLETED	Dopamine Versus Norepinephrine Under General Anesthesia
NCT04702373	Phase 3	UNKNOWN	Training in Exercise Activities and Motion for Growth (TEAM 4 Growth) RCT
NCT05049590	Phase 3	COMPLETED	Acute Normovolemic Hemodilution in Complex Cardiac Surgery
NCT06406517	Phase 3	UNKNOWN	Comparative Effectiveness of Gadopiclenol for Evaluation of Adult Congenital Heart Anatomy and Hemodynamics
NCT06693674	Phase 3	RECRUITING	Effect of Sacubitril-Valsartan on Cardiac Structure and Function
NCT06955260	Phase 3	RECRUITING	SGLT2 Inhibition With Empagliflozin in Fontan Circulatory Failure
NCT00115375	Phase 2	COMPLETED	Platelet Aggregation Inhibition in Children on Clopidogrel (PICOLO)
NCT00350220	Phase 2	COMPLETED	Transfusion Strategies in Pediatric Cardiothoracic Surgery
NCT00374088	Phase 2	COMPLETED	N-Acetylcysteine in Neonatal Congenital Heart Surgery (INACT Study)
NCT00538785	Phase 2	COMPLETED	A Study to Evaluate MEDI-524 In Children With Hemodynamically Significant Congenital Heart Disease
NCT00770705	Phase 2	WITHDRAWN	Parenteral Phenoxybenzamine During Congenital Heart Disease Surgery
NCT00919945	Phase 2	TERMINATED	Impact of Early Enteral Feeding on Splanchnic Blood Flow After Surgery for Critical Heart Disease in the Newborn
NCT01063712	Phase 2	COMPLETED	Safety and Effectiveness of the Device Nit-Occlud® PDA-R
NCT01069510	Phase 2	COMPLETED	Spironolactone in Adult Congenital Heart Disease
NCT01189981	Phase 2	COMPLETED	Effect of eHealth Encouragements to Intensive Exercise in Adolescents With Congenital Heart Disease
NCT01330433	Phase 2	COMPLETED	Effects of CoSeal on Bleeding & Adhesions in Pediatric Heart Surgery
NCT01662037	Phase 2	COMPLETED	Bosentan Therapy in Children With Functional Single Ventricle
NCT01668264	Phase 2	UNKNOWN	Imaging Assessment of Diastolic Function
NCT01827059	Phase 2	UNKNOWN	Bosentan In Exercise Induced Pulmonary Arterial Hypertension in CongenitaL Heart diseasE
NCT01841177	Phase 2	COMPLETED	Evaluating Precision of Therapy - Milrinone
NCT02046135	Phase 2	TERMINATED	Sodium Bicarbonate to Prevent Acute Kidney Injury in Children Undergoing Cardiac Surgery
NCT02133573	Phase 2	COMPLETED	Randomized Trial of Maternal Progesterone Therapy
NCT02232399	Phase 2	COMPLETED	Is Levosimendan Superior to Milrinone Regarding Acute Kidney Injury After Cardiac Surgery for Congenital Heart Disease?
NCT02492269	Phase 2	COMPLETED	Stress Response and Neurodevelopmental Outcome After Cardiac Surgery Utilizing CPB in Children: A Prospective, Double Blinded and Randomized Study
NCT02564796	Phase 2	TERMINATED	Erythropoietin to Prevent Unnecessary Transfusions In Patients With Cyanotic CHD - A Prospective Control Trial
NCT02618824	Phase 2	UNKNOWN	Role of Terminal Warm Blood Cardioplegia as Myocardial Protection in the Use of Histidine-Tryptophan-Ketoglutarate Cardioplegia in Complex Congenital Heart Surgery
NCT02769624	Phase 2	TERMINATED	Acute Effects of Inhaled Treprostinil in Fontan Patients
NCT02877238	Phase 2	COMPLETED	Remote Preconditioning and Myocardial Protection
NCT03082716	Phase 2	COMPLETED	Custodiol Versus Blood Cardioplegaia in Paediatric Cardiac Surgery
NCT03425734	Phase 2	UNKNOWN	The Effect of Dexmedetomidine on Kidney Perfusion in Paediatric Patients
NCT04434001	Phase 2	TERMINATED	ZEPLAST- PED: ZEro_PLASma Trial in Small Infants Undergoing Cardiac Surgery
NCT04807621	Phase 2	UNKNOWN	Platelets or Fibrinogen as First-line Treatment for Bleeding During Pedatric Heart Surgery
NCT05717049	Phase 2	COMPLETED	Theophylline Effects in the Fontan Circulation
NCT06080074	Phase 2	RECRUITING	Multicenter Trial of ECMO in Children With Severe Cardiac Failure Using the Cardiohelp System
NCT07498803	Phase 2	NOT_YET_RECRUITING	Sota-ES - Sotatercept in Patients With Congenital Heart Disease and Eisenmenger´s Syndrome
NCT01698567	Phase 1	TERMINATED	Antithrombin III in Infants With Cardiopulmonary Bypass (CPB)
NCT02549625	Phase 1	COMPLETED	Phase I Safety and Feasibility Study of Intracoronary Delivery of Autologous Bone Marrow Derived Mononuclear Cells
NCT03417999	Phase 1	TERMINATED	Pharmacokinetic Study of Intranasal Dexmedetomidine in Pediatric Patients With Congenital Heart Disease
NCT03946462	Phase 1	WITHDRAWN	Nitric Oxide During CPB to Reduce AKI in Neonates

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for HDAC1 across ~30M SureChEMBL compounds — explore on Sugi Predict.