HDAC11

Summary

HDAC11 (histone deacetylase 11, HGNC:19086) is a protein-coding gene on chromosome 3p25.1, encoding Histone deacetylase 11 (Q96DB2). Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).

This gene encodes a class IV histone deacetylase. The encoded protein is localized to the nucleus and may be involved in regulating the expression of interleukin 10. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 79885 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 61 total
• Druggable target: yes — 28 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_024827

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19086
Approved symbol	HDAC11
Name	histone deacetylase 11
Location	3p25.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000163517
Ensembl biotype	protein_coding
OMIM	607226
Entrez	79885

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 24 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000295757, ENST00000402259, ENST00000402271, ENST00000404040, ENST00000404548, ENST00000405025, ENST00000405478, ENST00000416248, ENST00000418189, ENST00000425430, ENST00000433119, ENST00000434848, ENST00000437379, ENST00000446613, ENST00000455904, ENST00000458642, ENST00000475818, ENST00000487585, ENST00000495099, ENST00000498532, ENST00000522202, ENST00000861266, ENST00000861267, ENST00000861268, ENST00000861269, ENST00000861270, ENST00000861271, ENST00000861272, ENST00000967009, ENST00000967010

RefSeq mRNA: 3 — MANE Select: NM_024827 NM_001136041, NM_001330636, NM_024827

CCDS: CCDS2615, CCDS46760, CCDS82738

Canonical transcript exons

ENST00000295757 — 10 exons

Exon	Start	End
ENSE00001873521	13504468	13506416
ENSE00003486563	13502884	13502980
ENSE00003499345	13501871	13501933
ENSE00003527472	13504094	13504272
ENSE00003599879	13496736	13496852
ENSE00003640558	13498513	13498555
ENSE00003642473	13483464	13483564
ENSE00003656822	13481246	13481394
ENSE00003672509	13480306	13480349
ENSE00003678590	13500713	13500789

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 95.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.3249 / max 68.0356, expressed in 1539 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
35403	3.7464	1491
35404	0.5785	241

Top tissues by expression

286 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	95.74	gold quality
inferior vagus X ganglion	UBERON:0005363	95.71	gold quality
right testis	UBERON:0004534	95.69	gold quality
putamen	UBERON:0001874	95.29	gold quality
amygdala	UBERON:0001876	95.00	gold quality
caudate nucleus	UBERON:0001873	94.86	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.62	gold quality
nucleus accumbens	UBERON:0001882	94.44	gold quality
prefrontal cortex	UBERON:0000451	94.29	gold quality
spinal cord	UBERON:0002240	93.77	gold quality
globus pallidus	UBERON:0001875	93.69	gold quality
medial globus pallidus	UBERON:0002477	93.60	gold quality
ventral tegmental area	UBERON:0002691	93.53	gold quality
anterior cingulate cortex	UBERON:0009835	93.49	gold quality
cingulate cortex	UBERON:0003027	93.43	gold quality
right frontal lobe	UBERON:0002810	93.41	gold quality
subthalamic nucleus	UBERON:0001906	93.19	gold quality
lateral globus pallidus	UBERON:0002476	93.18	gold quality
superior vestibular nucleus	UBERON:0007227	92.82	gold quality
temporal lobe	UBERON:0001871	92.78	gold quality
testis	UBERON:0000473	92.76	gold quality
substantia nigra pars reticulata	UBERON:0001966	92.55	gold quality
Ammon’s horn	UBERON:0001954	92.32	gold quality
frontal cortex	UBERON:0001870	92.18	gold quality
telencephalon	UBERON:0001893	92.11	gold quality
apex of heart	UBERON:0002098	91.90	gold quality
neocortex	UBERON:0001950	91.84	gold quality
midbrain	UBERON:0001891	91.79	gold quality
substantia nigra	UBERON:0002038	91.65	gold quality
forebrain	UBERON:0001890	91.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.12

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

5 targets.

Target	Regulation
IL10	Repression
IL17A	Repression
MYC	Unknown
TNF	Repression
TNFSF4	Activation

miRNA regulators (miRDB)

57 targeting HDAC11, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-508-5P	99.41	64.25	1248
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-1257	98.97	68.02	1133
HSA-MIR-3196	98.96	63.91	326
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-655-5P	98.74	65.93	888

Literature-anchored findings (GeneRIF, showing 29)

• cloning and functional characterization (PMID:11948178)
• Fluorescence in situ hybridization analysis localized HDAC11 gene to chromosome 3p25, a region characterized by frequent gains and losses of chromosomal material in a number of various types of cancer. (PMID:16142391)
• the absence of tumour-specific somatic events in WNT7A and HDAC11 suggests that these genes are unlikely to have a classical tumour suppressor gene role in sporadic malignant pancreatic endocrine tumours (PMID:17201809)
• HDAC11 negatively regulated expression of the gene encoding interleukin 10 in antigen-presenting cells. (PMID:19011628)
• Cdt1 undergoes acetylation and is reversibly deacetylated by HDAC11 (PMID:19276081)
• We found a reduction of HDAC 11 mRNA and increased HDAC 2 levels in amyotrophic lateral sclerosis brain and spinal cord compared with controls. (PMID:20467334)
• HDAC11 associates with replication origins inhibits Cdt1-induced re-replication and suppresses MCM loading. (PMID:20980834)
• These results demonstrate for the first time that HDAC11 plays an essential role in regulating OX40L expression. (PMID:21239696)
• Data indicate a pronounced deregulation of HDAC genes HDAC9 and HDAC11 in patients with Philadelphia-negative chronic myeloproliferative neoplasms: essential thrombocythemia (ET), polycythemia vera (PV) and primary myelofibrosis (PMF). (PMID:21806350)
• High HDAC11 expression is associated with neoplasms. (PMID:23024001)
• Our study identified a group of cell cycle-promoting genes regulated by HDAC11. (PMID:28252645)
• Results showed that the high levels of HDAC11 and lower levels of p53 were detected in pituitary tumor cells. A negative correlation was detected between the data of HDAC11 and p53. (PMID:28782861)
• HDAC11 was initially identified as a negative regulator of the well-known anti-inflammatory cytokine IL-10. Hence, antagonizing HDAC11 activity may have anti-tumor potential, whereas activating HDAC11 may be useful to treat chronic inflammation or autoimmunity. (PMID:29222071)
• report in vitro profiling of HDAC11 deacylase activities (PMID:29336543)
• Mycobacterium tuberculosis infection disturbs the HDAC6/HDAC11 levels to induce IL-10 expression in macrophages. (PMID:29523311)
• The results indicated that HDAC11 was significantly expressed in human and mouse diabetic heart failure (DHF) hearts. (PMID:29655790)
• IL-10 expression was compromised in the peripheral B cells of allergic rhinitis (AR) patients. Inhibition of HDAC11 restored the IL-10 expression ability in the AR-B cells. We also found a negative correlation between HDAC11 and the expression of IL-10 in B cells; this fact indicates that HDAC11 interferes with the expression of IL-10 in B cells. (PMID:30007011)
• HDAC11 is a regulatory molecule in Th2 response and plays a critical role in the restriction of the biased IL-13 expression in CD4(+) T cells of the heart. (PMID:30063898)
• regulates type I interferon signaling through defatty-acylation of SHMT2 (PMID:30819897)
• Novel HDAC11 inhibitors suppress lung adenocarcinoma stem cell self-renewal and overcome drug resistance by suppressing Sox2. (PMID:32170113)
• Long noncoding RNA BCYRN1 promotes prostate cancer progression via elevation of HDAC11. (PMID:32705287)
• HDAC11 Regulates Glycolysis through the LKB1/AMPK Signaling Pathway to Maintain Hepatocellular Carcinoma Stemness. (PMID:33602787)
• HDAC11: a multifaceted histone deacetylase with proficient fatty deacylase activity and its roles in physiological processes. (PMID:33891374)
• HDAC11 activity contributes to MEK inhibitor escape in uveal melanoma. (PMID:35332245)
• A pan-cancer analysis identifies HDAC11 as an immunological and prognostic biomarker. (PMID:35657209)
• HDAC11 negatively regulates antifungal immunity by inhibiting Nos2 expression via binding with transcriptional repressor STAT3. (PMID:36087429)
• HDAC11: A novel target for improved cancer therapy. (PMID:37659201)
• HDAC11 Regulates Palmitate-induced NLRP3 Inflammasome Activation by Inducing YAP Expression in THP-1 Cells and PBMCs. (PMID:38366363)
• [Progress on the involvement of HDAC11 in the regulation of mammalian oocyte maturation and early embryonic development]. (PMID:38939938)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	hdac11	ENSDARG00000087573
mus_musculus	Hdac11	ENSMUSG00000034245
rattus_norvegicus	Hdac11	ENSRNOG00000006824
drosophila_melanogaster	HDAC11	FBGN0051119
caenorhabditis_elegans		WBGENE00007953

Paralogs (10): HDAC9 (ENSG00000048052), HDAC7 (ENSG00000061273), HDAC4 (ENSG00000068024), HDAC6 (ENSG00000094631), HDAC10 (ENSG00000100429), HDAC5 (ENSG00000108840), HDAC1 (ENSG00000116478), HDAC8 (ENSG00000147099), HDAC3 (ENSG00000171720), HDAC2 (ENSG00000196591)

Protein

Protein identifiers

Histone deacetylase 11 — Q96DB2 (reviewed: Q96DB2)

All UniProt accessions (14): B5MC52, B5MCQ6, B5MCS3, B5MCU6, B5MCV5, B5MD06, C9J528, C9JBI4, C9JEC8, Q96DB2, C9JMH0, E7ETT9, F8WF94, Q658J9

UniProt curated annotations — full annotation on UniProt →

Function. Responsible for 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.

Subunit / interactions. Interacts with HDAC6.

Subcellular location. Nucleus.

Tissue specificity. Weakly expressed in most tissues. Strongly expressed in brain, heart, skeletal muscle, kidney and testis.

Miscellaneous. Its activity is inhibited by trapoxin, a known histone deacetylase inhibitor.

Similarity. Belongs to the histone deacetylase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96DB2-1	1	yes
Q96DB2-2	2

RefSeq proteins (3): NP_001129513, NP_001317565, NP_079103* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000286	HDACs	Family
IPR023696	Ureohydrolase_dom_sf	Homologous_superfamily
IPR023801	His_deacetylse_dom	Domain
IPR037138	His_deacetylse_dom_sf	Homologous_superfamily
IPR044150	HDAC_classIV	Domain

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), 1 shown:

• N(6)-acetyl-L-lysyl-[histone] + H2O = L-lysyl-[histone] + acetate (RHEA:58196)

UniProt features (8 total): sequence conflict 3, splice variant 2, chain 1, region of interest 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96DB2-F1	92.74	0.85

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): 143

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-2122947	NOTCH1 Intracellular Domain Regulates Transcription
R-HSA-2644606	Constitutive Signaling by NOTCH1 PEST Domain Mutants
R-HSA-2894862	Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
R-HSA-350054	Notch-HLH transcription pathway
R-HSA-9976102	Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)

MSigDB gene sets: 106 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, PID_HDAC_CLASSI_PATHWAY, REACTOME_SIGNALING_BY_NOTCH, GCANCTGNY_MYOD_Q6, CAGCTG_AP4_Q5, PATIL_LIVER_CANCER, JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, SMID_BREAST_CANCER_LUMINAL_B_UP, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, DELASERNA_MYOD_TARGETS_UP, GOBP_CHROMATIN_REMODELING, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, CUI_TCF21_TARGETS_2_UP, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION

GO Biological Process (2): chromatin organization (GO:0006325), epigenetic regulation of gene expression (GO:0040029)

GO Molecular Function (6): histone deacetylase activity (GO:0004407), DNA-binding transcription factor binding (GO:0140297), histone deacetylase activity, hydrolytic mechanism (GO:0141221), protein binding (GO:0005515), hydrolase activity (GO:0016787), protein lysine deacetylase activity (GO:0033558)

GO Cellular Component (3): histone deacetylase complex (GO:0000118), nucleus (GO:0005634), plasma membrane (GO:0005886)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Signaling by NOTCH1	1
Signaling by NOTCH1 PEST Domain Mutants in Cancer	1
Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer	1
Generic Transcription Pathway	1
Differentiation of T cells	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular component organization	1
chromatin remodeling	1
regulation of gene expression	1
protein lysine deacetylase activity	1
histone modifying activity	1
transcription factor binding	1
histone deacetylase activity	1
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	1
binding	1
catalytic activity	1
deacetylase activity	1
catalytic activity, acting on a protein	1
nucleoplasm	1
nuclear protein-containing complex	1
catalytic complex	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1938 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HDAC11	HDAC6	Q9UBN7	850
HDAC11	SIRT1	Q96EB6	840
HDAC11	ASPN	Q9BXN1	807
HDAC11	TAF1	P21675	758
HDAC11	SIN3A	Q96ST3	745
HDAC11	SIRT7	Q9NRC8	745
HDAC11	BRD2	P25440	725
HDAC11	KAT2B	Q92831	722
HDAC11	SIRT2	Q8IXJ6	720
HDAC11	SIRT4	Q9Y6E7	709
HDAC11	NCOR1	O75376	702
HDAC11	EP300	Q09472	700
HDAC11	RBBP4	P31149	693
HDAC11	SIRT6	Q8N6T7	686
HDAC11	SIRT5	Q9NXA8	635

IntAct

20 interactions, top by confidence:

A	B	Type	Score
DDX20	GEMIN4	psi-mi:“MI:0914”(association)	0.910
SMN1	GEMIN4	psi-mi:“MI:0914”(association)	0.790
GEMIN4	SMN1	psi-mi:“MI:0914”(association)	0.790
HDAC11	CLUH	psi-mi:“MI:0914”(association)	0.640
NRM	HDAC11	psi-mi:“MI:0915”(physical association)	0.560
HDAC11	HSD17B11	psi-mi:“MI:0915”(physical association)	0.560
HDAC11	GEMIN4	psi-mi:“MI:0914”(association)	0.460
HDAC11	HDAC6	psi-mi:“MI:0915”(physical association)	0.400
HDAC11	MAPK6	psi-mi:“MI:0915”(physical association)	0.370
HDAC11	CCDC22	psi-mi:“MI:0914”(association)	0.350
HDAC11	AGPS	psi-mi:“MI:0914”(association)	0.350
DICER1	GEMIN4	psi-mi:“MI:0914”(association)	0.350
NRM	HDAC11	psi-mi:“MI:0915”(physical association)	0.000
wzzE	HDAC11	psi-mi:“MI:0915”(physical association)	0.000
NELFCD	HDAC11	psi-mi:“MI:0915”(physical association)	0.000
CDKN1A	HDAC11	psi-mi:“MI:0915”(physical association)	0.000
PHYHIP	HDAC11	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (188): PAXBP1 (Affinity Capture-MS), ATG2B (Affinity Capture-MS), GCFC2 (Affinity Capture-MS), RSRC1 (Affinity Capture-MS), TFIP11 (Affinity Capture-MS), OSBPL3 (Affinity Capture-MS), WDR45 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), C16orf62 (Affinity Capture-MS), CCT2 (Affinity Capture-MS), MTMR3 (Affinity Capture-MS), ADD3 (Affinity Capture-MS), CALCOCO2 (Affinity Capture-MS), CLUH (Affinity Capture-MS), CCT6A (Affinity Capture-MS)

ESM2 similar proteins: A1L1L6, B1H369, B1WC68, O00764, O35331, O46560, O54956, O95803, P10155, P38024, P52848, P56965, P58710, P81799, P82197, Q02353, Q0II59, Q0VCB2, Q2HJF8, Q2QNG7, Q3SZM9, Q3U129, Q3UHN9, Q4R4U1, Q5R5F8, Q5U4X8, Q5ZM83, Q6GPA7, Q6GQK9, Q6GV29, Q6NVC5, Q7SXM0, Q80YV4, Q8BG51, Q8IXI2, Q8K183, Q8VH37, Q91WA3, Q923S8, Q969T7

Diamond homologs: B1H369, B1WC68, O09106, O13298, O15379, O17695, O22446, O30107, O42227, O59702, O88895, P32561, P39067, P53096, P56517, P56518, P56519, P56520, P56521, P64375, P64376, P70288, Q09440, Q0VCB2, Q12214, Q13547, Q28DV3, Q2QWU2, Q32PJ8, Q4QQW4, Q4SFA0, Q55BW2, Q55FN5, Q5HF39, Q5RAG0, Q5RB76, Q6G8J2, Q6GFX3, Q6GPA7, Q6IRL9

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
HDAC11	“down-regulates activity”	BRD2	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2005 predictions. Top by Δscore:

Variant	Effect	Δscore
3:13481237:A:AG	acceptor_gain	1.0000
3:13481238:C:G	acceptor_gain	1.0000
3:13481243:TA:T	acceptor_loss	1.0000
3:13481244:A:C	acceptor_loss	1.0000
3:13481394:GGTA:G	donor_loss	1.0000
3:13481395:G:GG	donor_gain	1.0000
3:13481396:T:G	donor_loss	1.0000
3:13500707:CCGCA:C	acceptor_loss	1.0000
3:13500708:CGCAG:C	acceptor_loss	1.0000
3:13500709:GCAG:G	acceptor_loss	1.0000
3:13500710:CAG:C	acceptor_loss	1.0000
3:13500711:A:AG	acceptor_gain	1.0000
3:13500711:AG:A	acceptor_gain	1.0000
3:13500711:AGG:A	acceptor_gain	1.0000
3:13500711:AGGG:A	acceptor_gain	1.0000
3:13500712:G:GG	acceptor_gain	1.0000
3:13500712:G:T	acceptor_loss	1.0000
3:13500712:GG:G	acceptor_gain	1.0000
3:13500712:GGG:G	acceptor_gain	1.0000
3:13500712:GGGG:G	acceptor_gain	1.0000
3:13501865:T:A	acceptor_gain	1.0000
3:13501866:GGCA:G	acceptor_loss	1.0000
3:13501867:GCA:G	acceptor_loss	1.0000
3:13501869:A:AG	acceptor_gain	1.0000
3:13501870:G:GG	acceptor_gain	1.0000
3:13501870:GT:G	acceptor_gain	1.0000
3:13501870:GTTT:G	acceptor_gain	1.0000
3:13501931:CAGGT:C	donor_loss	1.0000
3:13501933:GGTG:G	donor_loss	1.0000
3:13501934:G:C	donor_loss	1.0000

AlphaMissense

2263 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:13500724:C:G	H142D	1.000
3:13500732:C:G	C144W	1.000
3:13500754:T:C	F152L	1.000
3:13500756:C:A	F152L	1.000
3:13500756:C:G	F152L	1.000
3:13481352:T:C	F37L	0.999
3:13481354:T:A	F37L	0.999
3:13481354:T:G	F37L	0.999
3:13481366:A:C	K41N	0.999
3:13481366:A:T	K41N	0.999
3:13481367:T:A	W42R	0.999
3:13481367:T:C	W42R	0.999
3:13498551:C:A	N136K	0.999
3:13498551:C:G	N136K	0.999
3:13500731:G:A	C144Y	0.999
3:13500757:T:C	C153R	0.999
3:13500758:G:A	C153Y	0.999
3:13500759:T:G	C153W	0.999
3:13501923:A:T	D181V	0.999
3:13504225:G:C	D261H	0.999
3:13504226:A:C	D261A	0.999
3:13504226:A:G	D261G	0.999
3:13504226:A:T	D261V	0.999
3:13504227:C:A	D261E	0.999
3:13504227:C:G	D261E	0.999
3:13504549:T:C	Y304H	0.999
3:13481346:C:G	H35D	0.998
3:13483524:T:C	L71P	0.998
3:13496827:G:C	R115P	0.998
3:13500721:T:C	F141L	0.998

dbSNP variants (sampled 300 via entrez): RS1000097992 (3:13493976 A>G), RS1000337717 (3:13485990 G>A,C,T), RS1000361842 (3:13502144 C>T), RS1000401841 (3:13495971 C>A), RS1000524228 (3:13490455 C>A,T), RS1000571081 (3:13491325 G>T), RS1000621539 (3:13480371 C>A,T), RS1000850855 (3:13479953 G>A), RS1000892704 (3:13479840 G>A,C,T), RS1000921363 (3:13491066 A>T), RS1000942880 (3:13479610 C>T), RS1001127494 (3:13485403 G>A,T), RS1001392154 (3:13487122 G>A,C), RS1001640523 (3:13502202 G>A,C), RS1001647672 (3:13498389 C>A,T)

Disease associations

OMIM: gene MIM:607226 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST000817_45	Height	7.000000e-10
GCST004067_190	Hip circumference adjusted for BMI	2.000000e-06
GCST004067_77	Hip circumference adjusted for BMI	2.000000e-08
GCST005951_48	Body mass index	5.000000e-08
GCST008732_1	Ulcerative colitis	7.000000e-06
GCST012226_604	Waist circumference adjusted for body mass index	1.000000e-08
GCST90020028_706	Hip circumference adjusted for BMI	1.000000e-09
GCST90020028_707	Hip circumference adjusted for BMI	2.000000e-11
GCST90020028_708	Hip circumference adjusted for BMI	4.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference
EFO:0004340	body mass index
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (3): CHEMBL2093865 (PROTEIN FAMILY), CHEMBL3310 (SINGLE PROTEIN), CHEMBL6193802 (PROTEIN-PROTEIN INTERACTION)

Molecules with ChEMBL bioactivity

28 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 437,477 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL118	CELECOXIB	4	112,844
CHEMBL1469	PHENYLBUTANOIC ACID	4	37,081
CHEMBL1746	SODIUM PHENYLBUTYRATE	4	5,577
CHEMBL343448	ROMIDEPSIN	4	12,963
CHEMBL408513	BELINOSTAT	4	7,765
CHEMBL483254	PANOBINOSTAT	4	11,666
CHEMBL98	VORINOSTAT	4	50,361
CHEMBL1213492	GIVINOSTAT	4	2,827
CHEMBL140	CURCUMIN	3	93,882
CHEMBL145	CAFFEIC ACID	3	36,305
CHEMBL1851943	PRACINOSTAT	3	1,998
CHEMBL235191	TACEDINALINE	3	2,950
CHEMBL27759	ENTINOSTAT	3	6,584
CHEMBL3621988	TUCIDINOSTAT	3	2,182
CHEMBL2103863	ABEXINOSTAT	3	2,195
CHEMBL1801250	NANATINOSTAT	2	754
CHEMBL191482	AR-42	2	2,061
CHEMBL284616	CHLOROGENIC ACID	2	41,945
CHEMBL356066	DACINOSTAT	2	3,050
CHEMBL3622533	FIMEPINOSTAT	2	2,487
CHEMBL2105763	QUISINOSTAT	2
CHEMBL272980	MOCETINOSTAT	2
CHEMBL4283683	DOMATINOSTAT	2
CHEMBL353581	PYROXAMIDE	1
CHEMBL598797	CUDC-101	1
CHEMBL609583	R-306465	1
CHEMBL96	GAMMA-AMINOBUTYRIC ACID	1
CHEMBL99	TRICHOSTATIN	1

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

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

Target class: enzyme — 3.5.1.- Histone deacetylases (HDACs)

Most potent curated ligand interactions (5 total), top 5:

Ligand	Action	Affinity	Parameter
quisinostat	Inhibition	9.43	pIC50
fimepinostat	Inhibition	8.27	pIC50
vorinostat	Inhibition	7.44	pKi
KA1010	Inhibition	6.23	pIC50
SS-208	Inhibition	5.29	pIC50

Binding affinities (BindingDB)

64 measured of 72 human assays (72 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
Quinolone-based HDAC inhibitor 4i	IC50	0.1 nM
Quinolone-based HDAC inhibitor 4j	IC50	1.5 nM
CHEBI:46024	IC50	4.9 nM
R-TSA	IC50	5.76 nM
Quinolone-based HDAC inhibitor 4o	IC50	10 nM
Quinolone-based HDAC inhibitor 4p	IC50	28 nM
Quinolone-based HDAC inhibitor 4r	IC50	28 nM
Quinolone-based HDAC inhibitor 4a	IC50	32 nM
Quinolone-based HDAC inhibitor 4k	IC50	32 nM
Quinolone-based HDAC inhibitor 4l	IC50	32 nM
(2E)-N-hydroxy-3-[3-(phenylsulfamoyl)phenyl]prop-2-enamide	IC50	34 nM
Quinolone-based HDAC inhibitor 4c	IC50	39 nM
Quinolone-based HDAC inhibitor 4v	IC50	39 nM
Quinolone-based HDAC inhibitor 4q	IC50	40 nM
Quinolone-based HDAC inhibitor 4h	IC50	42 nM
3-(furan-3-yl)-N-[[4-(hydroxycarbamoyl)phenyl]methyl]-5-(4-hydroxyphenyl)-1H-pyrrole-2-carboxamide	IC50	49.9 nM	US-8685992: Histone deacetylase inhibitors based simultaneously on trisubstituted 1H-pyrroles and aromatic and heteroaromatic spacers
N-[[4-[(2-aminophenyl)carbamoyl]phenyl]methyl]-3-(4-hydroxyphenyl)-5-thiophen-3-yl-1H-pyrrole-2-carboxamide	IC50	71 nM	US-8685992: Histone deacetylase inhibitors based simultaneously on trisubstituted 1H-pyrroles and aromatic and heteroaromatic spacers
N-hydroxy-7-[pyridin-2-yl(quinolin-2-yl)amino]heptanamide	IC50	71 nM	US-8748458: Scriptaid isosteres and their use in therapy
(S)-N1-(3-(1H-indol-3-yl)-1-oxo-1-(p-tolylamino)propan-2-yl)-N4-hydroxyterephthalamide (12m)	IC50	74 nM
Quinolone-based HDAC inhibitor 4m	IC50	75 nM
(S)-N1-(3-(1H-indol-3-yl)-1-((4-iodophenyl)amino)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12l)	IC50	78 nM
3-(4-methoxyphenyl)-5-phenyl-N-[[4-(2-sulfanylethylcarbamoyl)phenyl]methyl]-1H-pyrrole-2-carboxamide	IC50	84.2 nM	US-8685992: Histone deacetylase inhibitors based simultaneously on trisubstituted 1H-pyrroles and aromatic and heteroaromatic spacers
Quinolone-based HDAC inhibitor 4u	IC50	85 nM
Quinolone-based HDAC inhibitor 4g	IC50	90 nM
(S,E)-N-hydroxy-3-(3-(N-(2-(naphthalen-1-ylamino)-2-oxo-1-phenylethyl)sulfamoyl)phenyl)acrylamide (10s)	IC50	93 nM
Quinolone-based HDAC inhibitor 4w	IC50	95 nM
(S)-N1-(1-((4-bromophenyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12k)	IC50	96 nM
MGCD-0103	IC50	102 nM	US-9409858: Selective histone deactylase 6 inhibitors
Quinolone-based HDAC inhibitor 4d	IC50	120 nM
(S)-N1-(1-((4-chlorophenyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12j)	IC50	150 nM
Quinolone-based HDAC inhibitor 4n	IC50	150 nM
N-hydroxy-4-[(3-oxo-[1,2]thiazolo[5,4-b]pyridin-2-yl)methyl]benzamide	IC50	175 nM	US-10011611: Histone deacetylase inhibitors and methods for use thereof
N-[[4-[(2-aminophenyl)carbamoyl]phenyl]methyl]-3-(furan-3-yl)-5-(4-hydroxyphenyl)-1H-pyrrole-2-carboxamide	IC50	184 nM	US-8685992: Histone deacetylase inhibitors based simultaneously on trisubstituted 1H-pyrroles and aromatic and heteroaromatic spacers
(S)-N1-(1-((3-bromophenyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12g)	IC50	189 nM
(S)-N1-(1-((4-fluorophenyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12i)	IC50	202 nM
S-TSA	IC50	206 nM
(S)-N1-(3-(1H-indol-3-yl)-1-((naphthalen-1-ylmethyl)amino)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12d)	IC50	225 nM
(S)-N1-(3-(1H-indol-3-yl)-1-oxo-1-(propylamino)propan-2-yl)-N4-hydroxyterephthalamide (8a)	IC50	227 nM
Quinolone-based HDAC inhibitor 4t	IC50	230 nM
(S)-N1-(1-((3-fluorophenyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12e)	IC50	234 nM
Quinolone-based HDAC inhibitor 4b	IC50	270 nM
(S)-N1-(3-(1H-indol-3-yl)-1-oxo-1-(phenethylamino)propan-2-yl)-N4-hydroxyterephthalamide (12c)	IC50	301 nM
Quinolone-based HDAC inhibitor 4s	IC50	330 nM
3-(4-fluorophenyl)-N-[[4-(hydroxycarbamoyl)phenyl]methyl]-5-pyridin-3-yl-1H-pyrrole-2-carboxamide	IC50	332 nM	US-8685992: Histone deacetylase inhibitors based simultaneously on trisubstituted 1H-pyrroles and aromatic and heteroaromatic spacers
(S)-N1-(1-((4-ethoxyphenyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12o)	IC50	335 nM
(S)-N1-(1-(benzylamino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12b)	IC50	346 nM
(S)-N1-(1-((3-chlorophenyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N4-hydroxyterephthalamide (12f)	IC50	360 nM
(S)-N1-(3-(1H-indol-3-yl)-1-oxo-1-(phenylamino)propan-2-yl)-N4-hydroxyterephthalamide (12a)	IC50	361 nM
Quinolone-based HDAC inhibitor 4f	IC50	390 nM
Quinolone-based HDAC inhibitor 4e	IC50	410 nM

ChEMBL bioactivities

3635 potent at pChembl≥5 of 4006 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
10.15	Ki	0.07	nM	QUISINOSTAT
10.00	IC50	0.1	nM	CHEMBL3329621
9.77	IC50	0.17	nM	CHEMBL5433552
9.70	IC50	0.2	nM	CHEMBL3329622
9.70	IC50	0.2	nM	CHEMBL2371007
9.70	IC50	0.2	nM	CHEMBL5395502
9.70	IC50	0.2	nM	CHEMBL1793811
9.70	IC50	0.2	nM	CHEMBL1793991
9.70	IC50	0.2	nM	CHEMBL1793985
9.52	IC50	0.3	nM	ROMIDEPSIN
9.52	IC50	0.3	nM	CHEMBL2370998
9.52	IC50	0.3	nM	CHEMBL5199116
9.52	IC50	0.3	nM	CHEMBL5170036
9.52	IC50	0.3	nM	FR-135313
9.52	IC50	0.3	nM	CHEMBL1793822
9.46	IC50	0.35	nM	VORINOSTAT
9.43	IC50	0.37	nM	QUISINOSTAT
9.40	IC50	0.4	nM	CHEMBL2371000
9.40	IC50	0.4	nM	QUISINOSTAT
9.40	IC50	0.4	nM	CHEMBL1793816
9.08	IC50	0.83	nM	PANOBINOSTAT
9.05	IC50	0.9	nM	CHEMBL5618885
9.05	IC50	0.9	nM	CHEMBL605110
9.02	IC50	0.95	nM	CHEMBL595479
9.00	IC50	1	nM	CHEMBL3356916
9.00	IC50	1	nM	CHEMBL3758184
9.00	IC50	1	nM	APICIDIN
9.00	IC50	1	nM	CHEMBL2371003
9.00	IC50	1	nM	CHEMBL4130288
9.00	IC50	1	nM	ROMIDEPSIN
9.00	IC50	1	nM	CHEMBL4467135
9.00	IC50	1	nM	CHEMBL595711
9.00	IC50	1	nM	CHEMBL595910
9.00	IC50	1	nM	CHEMBL1793947
9.00	IC50	1	nM	CHEMBL1793810
9.00	IC50	1	nM	CHEMBL1793823
8.99	IC50	1.03	nM	CHEMBL1214760
8.98	IC50	1.05	nM	CHEMBL594544
8.92	IC50	1.2	nM	CHEMBL604796
8.92	IC50	1.2	nM	CHEMBL608416
8.92	IC50	1.2	nM	CHEMBL594544
8.89	IC50	1.3	nM	CHEMBL1793992
8.85	IC50	1.4	nM	CHEMBL99661
8.85	IC50	1.42	nM	TRICHOSTATIN
8.82	IC50	1.5	nM	TRICHOSTATIN
8.82	IC50	1.5	nM	CHEMBL5280445
8.82	IC50	1.5	nM	CHEMBL594743
8.82	IC50	1.5	nM	CHEMBL593846
8.82	IC50	1.5	nM	CHEMBL594542
8.80	IC50	1.6	nM	PANOBINOSTAT

PubChem BioAssay actives

2563 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-(4-methylphenyl)sulfonylpiperazin-1-yl]-1,3-thiazole-5-carboxamide	1941741: Inhibition of HDAC (unknown origin)	ic50	0.0001	uM
N-hydroxy-2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]pyrimidine-5-carboxamide	1236452: Inhibition of human HDAC11	ki	0.0001	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	1188986: Inhibition of HDAC11 (unknown origin) incubated for 3 hrs in presence of BSA and DTT by fluorescence assay	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
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	1188986: Inhibition of HDAC11 (unknown origin) incubated for 3 hrs in presence of BSA and DTT by fluorescence assay	ic50	0.0002	uM
7-[4-[[4-[3-(tert-butylsulfamoyl)anilino]-5-methylpyrimidin-2-yl]amino]-2-fluorophenoxy]-N-hydroxyheptanamide	2031064: Inhibition of HDAC in human HeLa cells nuclear extract incubated for 30 mins by multiplate reader analysis	ic50	0.0002	uM
7-[4-[[4-[3-(tert-butylsulfamoyl)anilino]-5-methylpyrimidin-2-yl]amino]phenoxy]-N-hydroxyheptanamide	2031064: Inhibition of HDAC in human HeLa cells nuclear extract incubated for 30 mins by multiplate reader analysis	ic50	0.0002	uM
(9S,12R)-3-[(2S)-butan-2-yl]-9-(6-hydroxy-5-oxoheptyl)-6-[(1-methoxyindol-3-yl)methyl]-1,4,7,10-tetrazabicyclo[10.4.0]hexadecane-2,5,8,11-tetrone	1847765: Inhibition of HDAC (unknown origin)	ic50	0.0003	uM
(9S,12R)-3-[(2S)-butan-2-yl]-6-(1H-indol-3-ylmethyl)-9-(5-oxoheptyl)-1,4,7,10-tetrazabicyclo[10.4.0]hexadecane-2,5,8,11-tetrone	1847765: Inhibition of HDAC (unknown origin)	ic50	0.0003	uM
(3S,6S,9S,12R)-3-[(2S)-butan-2-yl]-9-(7-hydroxy-6-oxooctyl)-6-[(1-methoxyindol-3-yl)methyl]-1,4,7,10-tetrazabicyclo[10.4.0]hexadecane-2,5,8,11-tetrone	90356: Inhibitory concentration against human Histone deacetylase in Hela cells	ic50	0.0003	uM
N-hydroxy-2-[4-[(E)-1-hydroxy-4-(4-phenylphenyl)but-3-en-2-yl]piperazin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0009	uM
N-hydroxy-2-[4-[(E)-1-hydroxy-4-(4-methoxyphenyl)but-3-en-2-yl]piperazin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0009	uM
N-hydroxy-2-[4-[(E)-1-hydroxy-4-phenylbut-3-en-2-yl]piperazin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0010	uM
2-[4-[(E)-4-(4-fluorophenyl)-1-hydroxybut-3-en-2-yl]piperazin-1-yl]-N-hydroxypyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0010	uM
N-hydroxy-1,1-dimethyl-2-[5-(trifluoromethyl)-1,3-benzoxazol-2-yl]-3H-isoindole-4-carboxamide	1496344: Inhibition of full length recombinant human HDAC11 expressed in baculoviral expression system using FAM-RHKK as substrate by electrophoretic mobility shift assay	ic50	0.0010	uM
(3S,6R,9S,12R)-3-[(2S)-butan-2-yl]-6-[(1-methoxyindol-2-yl)methyl]-9-(6-oxooctyl)-1,4,10-triazabicyclo[10.4.0]hexadecane-2,5,8,11-tetrone	1622995: Inhibition of HDAC (unknown origin)	ic50	0.0010	uM
N-hydroxy-6-[(2S,5S,8S,11S)-8-(1H-indol-3-ylmethyl)-2-methyl-11-(2-methylpropyl)-3,6,9,13-tetraoxo-1,4,7,10-tetrazacyclotridec-5-yl]hexanamide	447991: Inhibition of HDAC in human HeLa cell nuclear extract after 30 mins by fluorimetric assay	ic50	0.0010	uM
N-hydroxy-2-[4-[(E)-1-hydroxy-4-(4-methylphenyl)but-3-en-2-yl]piperazin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0010	uM
6-[(5S,8S,11R)-11-[(2S)-butan-2-yl]-8-(1H-indol-2-ylmethyl)-3,6,9,13-tetraoxo-1,4,7,10-tetrazacyclotridec-5-yl]-N-hydroxyhexanamide	487230: Inhibition of HDAC in human HeLa cells	ic50	0.0010	uM
7-[4-[4-[[[(2S,3R,4S,6R)-2-[[(2R,4R,5R,6R,8R,11R,12S,19R,20R)-11-ethyl-4-methoxy-2,4,6,8,12,19-hexamethyl-7,9,14-trioxo-10,13-dioxa-15,18-diazatricyclo[10.6.2.015,20]icos-1(18)-en-5-yl]oxy]-3-hydroxy-6-methyloxan-4-yl]-methylamino]methyl]phenyl]triazol-1-yl]-N-hydroxyheptanamide	499799: Inhibition of HDAC in human HeLa cell nuclear extracts	ic50	0.0010	uM
(E)-N-hydroxy-3-[4-oxo-1’-(2-phenylethyl)spiro[3H-chromene-2,3’-piperidine]-6-yl]prop-2-enamide	1273866: Inhibition of HDAC in human HeLa cells nuclear extract using Fluor de lys as substrate after 15 mins by fluorometric analysis	ic50	0.0010	uM
2-[4-[(E)-4-(3-fluorophenyl)-1-hydroxybut-3-en-2-yl]piperazin-1-yl]-N-hydroxypyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0012	uM
2-[4-[(E)-4-(4-chlorophenyl)-1-hydroxybut-3-en-2-yl]piperazin-1-yl]-N-hydroxypyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0012	uM
N’-hydroxy-N-[(2R)-4-(methylamino)-3-oxo-1-phenylbutan-2-yl]octanediamide	90195: Concentration required to inhibit Histone Deacetylase (HDAC) from K562 erythroleukemia cells	ic50	0.0014	uM
(2E,4E,6R)-7-[4-(dimethylamino)phenyl]-N-hydroxy-4,6-dimethyl-7-oxohepta-2,4-dienamide	1273502: Inhibition of HDAC in human HeLa cell nuclear extract using BML-KI104 Fluor de Lys as substrate by fluorescence-based assay	ic50	0.0014	uM
N-hydroxy-2-[4-(naphthalen-2-ylmethyl)piperazin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0015	uM
N-hydroxy-2-[4-[(E)-1-methoxy-4-phenylbut-3-en-2-yl]piperazin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0015	uM
N-hydroxy-2-[4-[[[(E)-1-hydroxy-4-phenylbut-3-en-2-yl]amino]methyl]piperidin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0015	uM
N-(1,3-benzothiazol-2-yl)-1-[5-(hydroxyamino)-5-oxopentyl]-4-oxoquinoline-3-carboxamide	1794854: HDAC Activity screening from Article 10.3109/14756366.2013.827675: “Quinolone-based HDAC inhibitors.”	ic50	0.0015	uM
N-hydroxy-2-[4-[(E)-4-phenylbut-3-en-2-yl]piperazin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0017	uM
N-hydroxy-6-[4-(6-methoxynaphthalen-2-yl)triazol-1-yl]hexanamide	382342: Inhibition of human HDAC in HeLa cells by flour de lys assay	ic50	0.0018	uM
N-hydroxy-6-[4-(3-phenylphenyl)triazol-1-yl]hexanamide	382342: Inhibition of human HDAC in HeLa cells by flour de lys assay	ic50	0.0019	uM
2-[2-[2-[[(2E)-3-(3-bromo-4-hydroxyphenyl)-2-hydroxyiminopropanoyl]amino]ethyldisulfanyl]ethylamino]-2-oxoacetic acid	90530: Inhibitory concentration against isolated Histone deacetylase	ic50	0.0020	uM
(3S,6S,9S,12R)-3-[(2S)-butan-2-yl]-6-(1H-indol-3-ylmethyl)-9-(6-oxooctyl)-1,4,7,10-tetrazabicyclo[10.4.0]hexadecane-2,5,8,11-tetrone	81887: Inhibitory activity against histone deacetylase (HDAC) enzyme derived from partially purified extracts of human HeLa cells using [3H]11 as radioligand	ic50	0.0020	uM
N-hydroxy-1,1-dimethyl-2-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]-3H-isoindole-4-carboxamide	1496344: Inhibition of full length recombinant human HDAC11 expressed in baculoviral expression system using FAM-RHKK as substrate by electrophoretic mobility shift assay	ic50	0.0020	uM
6-[4-[[5-chloro-4-(4-chloroanilino)pyrimidin-2-yl]amino]pyrazol-1-yl]-N-hydroxyhexanamide	1550094: Inhibition of HDAC in human HeLa nuclear extract using Boc-Lys(acetyl)-AMC as substrate preincubated for 5 mins followed by substrate addition and measured after 30 mins by fluorescence assay	ic50	0.0020	uM
7-[4-[[5-chloro-4-(4-chloroanilino)pyrimidin-2-yl]amino]pyrazol-1-yl]-N-hydroxyheptanamide	1550094: Inhibition of HDAC in human HeLa nuclear extract using Boc-Lys(acetyl)-AMC as substrate preincubated for 5 mins followed by substrate addition and measured after 30 mins by fluorescence assay	ic50	0.0020	uM
N-hydroxy-2-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]-1,3-dihydroisoindole-4-carboxamide	1496344: Inhibition of full length recombinant human HDAC11 expressed in baculoviral expression system using FAM-RHKK as substrate by electrophoretic mobility shift assay	ic50	0.0020	uM
N-hydroxy-1,1-dimethyl-2-([1,3]oxazolo[4,5-b]pyridin-2-yl)-3H-isoindole-4-carboxamide	1496344: Inhibition of full length recombinant human HDAC11 expressed in baculoviral expression system using FAM-RHKK as substrate by electrophoretic mobility shift assay	ic50	0.0020	uM
4-[(E)-3-[[(2S)-1-(4-bromoanilino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl]amino]-3-oxoprop-1-enyl]-N-hydroxybenzamide	1390020: Inhibition of HDAC in human HeLa cell nuclear extract using Boc-Lys (acetyl)-AMC as substrate preincubated for 5 mins followed by substrate addition measured after 30 mins by fluorescence assay	ic50	0.0020	uM
4-[(E)-3-[[(2S)-1-(4-fluoroanilino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl]amino]-3-oxoprop-1-enyl]-N-hydroxybenzamide	1390020: Inhibition of HDAC in human HeLa cell nuclear extract using Boc-Lys (acetyl)-AMC as substrate preincubated for 5 mins followed by substrate addition measured after 30 mins by fluorescence assay	ic50	0.0020	uM
2-(6-ethoxy-3-pyridinyl)-N-[7-(hydroxyamino)-7-oxoheptyl]-9-(2-methoxy-3-pyridinyl)-8-oxo-7H-purine-6-carboxamide	2079009: Inhibition of HDAC in human HeLa cells nuclear extract	ic50	0.0020	uM
2-[4-[(E)-4-(2-fluorophenyl)-1-hydroxybut-3-en-2-yl]piperazin-1-yl]-N-hydroxypyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0020	uM
N-hydroxy-2-(4-naphthalen-2-ylsulfonylpiperazin-1-yl)pyrimidine-5-carboxamide	454862: Inhibition of human HDAC11	ic50	0.0021	uM
N-hydroxy-7-[5-(4-methoxyphenyl)-1,3-oxazol-2-yl]heptanamide	316872: Inhibition of HDAC from human K562 cells	ic50	0.0021	uM
N-hydroxy-6-[4-(4-methoxyphenyl)triazol-1-yl]hexanamide	382342: Inhibition of human HDAC in HeLa cells by flour de lys assay	ic50	0.0021	uM
tert-butyl (8R,9R,12S)-12-[[6-(hydroxyamino)-6-oxohexyl]carbamoyl]-9-(2-methylpropyl)-2-oxa-11-azabicyclo[12.2.2]octadeca-1(16),14,17-triene-8-carboxylate	90195: Concentration required to inhibit Histone Deacetylase (HDAC) from K562 erythroleukemia cells	ic50	0.0021	uM
N-hydroxy-6-(4-quinolin-2-yltriazol-1-yl)hexanamide	382342: Inhibition of human HDAC in HeLa cells by flour de lys assay	ic50	0.0021	uM
N-hydroxy-2-[4-[(E)-1-hydroxy-4-[4-(trifluoromethyl)phenyl]but-3-en-2-yl]piperazin-1-yl]pyrimidine-5-carboxamide	454842: Inhibition of HDAC in human HeLa cells extractt	ic50	0.0021	uM
6-[4-(4-bromoanilino)-7-methoxyquinazolin-6-yl]oxy-N-hydroxyhexanamide	1720096: Inhibition of HDAC (unknown origin)	ic50	0.0022	uM

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Estradiol	decreases reaction, increases expression, affects expression	2
Valproic Acid	affects methylation, increases methylation	2
aristolochic acid I	increases expression	1
dicrotophos	decreases expression	1
pirinixic acid	increases activity, affects binding, decreases expression	1
sulforaphane	decreases expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Calcitriol	increases expression, affects cotreatment	1
Cisplatin	decreases expression	1
Curcumin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Methylcholanthrene	affects binding, increases reaction	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Asbestos, Crocidolite	decreases expression	1
Cadmium Chloride	decreases expression	1
Acrylamide	decreases expression	1
tert-Butylhydroperoxide	affects expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases expression	1

ChEMBL screening assays

1673 unique, capped per target: 1661 binding, 7 admet, 4 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

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SR04	HAP1 HDAC11 (-) 1	Cancer cell line	Male
CVCL_SR05	HAP1 HDAC11 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.