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KDM1A

gene
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Also known as KIAA0601BHC110LSD1

Summary

KDM1A (lysine demethylase 1A, HGNC:29079) is a protein-coding gene on chromosome 1p36.12, encoding Lysine-specific histone demethylase 1A (O60341). Histone demethylase that can demethylate both ‘Lys-4’ (H3K4me) and ‘Lys-9’ (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context.

This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 23028 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome (Definitive, ClinGen)
  • GWAS associations: 12
  • Clinical variants (ClinVar): 1,163 total — 7 pathogenic, 9 likely-pathogenic
  • Phenotypes (HPO): 98
  • Druggable target: yes — 38 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_001009999

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29079
Approved symbolKDM1A
Namelysine demethylase 1A
Location1p36.12
Locus typegene with protein product
StatusApproved
AliasesKIAA0601, BHC110, LSD1
Ensembl geneENSG00000004487
Ensembl biotypeprotein_coding
OMIM609132
Entrez23028

Gene structure

Transcript identifiers

Ensembl transcripts: 64 — 47 protein_coding, 13 retained_intron, 4 nonsense_mediated_decay

ENST00000356634, ENST00000400181, ENST00000465864, ENST00000481879, ENST00000494920, ENST00000602503, ENST00000685102, ENST00000685243, ENST00000686270, ENST00000686339, ENST00000686771, ENST00000686793, ENST00000686934, ENST00000687202, ENST00000688122, ENST00000688235, ENST00000688680, ENST00000688943, ENST00000689366, ENST00000689677, ENST00000689853, ENST00000689971, ENST00000690391, ENST00000690627, ENST00000690907, ENST00000691256, ENST00000691404, ENST00000691682, ENST00000691694, ENST00000691813, ENST00000692056, ENST00000692209, ENST00000692214, ENST00000692853, ENST00000692975, ENST00000693156, ENST00000874660, ENST00000874661, ENST00000874662, ENST00000874663, ENST00000874664, ENST00000919146, ENST00000919147, ENST00000919148, ENST00000919149, ENST00000919150, ENST00000919151, ENST00000919152, ENST00000919153, ENST00000919154, ENST00000919155, ENST00000919156, ENST00000919157, ENST00000919158, ENST00000919159, ENST00000919160, ENST00000919161, ENST00000954764, ENST00000954765, ENST00000954766, ENST00000954767, ENST00000954768, ENST00000954769, ENST00000954770

RefSeq mRNA: 5 — MANE Select: NM_001009999 NM_001009999, NM_001363654, NM_001410762, NM_001410763, NM_015013

CCDS: CCDS30627, CCDS53278, CCDS85939, CCDS90880, CCDS90881

Canonical transcript exons

ENST00000400181 — 21 exons

ExonStartEnd
ENSE000003885422303046923030634
ENSE000003885532307329223073403
ENSE000007591082306906123069151
ENSE000007591102306853923068681
ENSE000007591112305907323059167
ENSE000007591172305038723050520
ENSE000007591182304442723044486
ENSE000008597032305506923055161
ENSE000008597042305593223056038
ENSE000008597052305748423057565
ENSE000008597092307122523071359
ENSE000015487202301946823019947
ENSE000016413632306606023066071
ENSE000032843242308144623081573
ENSE000033241172307899023079177
ENSE000033345992307212423072197
ENSE000033736122307722823077360
ENSE000033866212308222023082366
ENSE000034409562307955323079667
ENSE000036192192305376123053839
ENSE000039040412308317923083689

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 98.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 67.9437 / max 806.8042, expressed in 1817 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
133366.00731817
13321.3783747
13360.5581290

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402398.68gold quality
ventricular zoneUBERON:000305398.34gold quality
cortical plateUBERON:000534398.24gold quality
embryoUBERON:000092298.05gold quality
right testisUBERON:000453497.76gold quality
left testisUBERON:000453397.73gold quality
testisUBERON:000047396.84gold quality
type B pancreatic cellCL:000016995.82silver quality
stromal cell of endometriumCL:000225595.45gold quality
adenohypophysisUBERON:000219695.29gold quality
right ovaryUBERON:000211895.17gold quality
right uterine tubeUBERON:000130295.03gold quality
left ovaryUBERON:000211994.98gold quality
pituitary glandUBERON:000000794.89gold quality
body of uterusUBERON:000985394.33gold quality
endocervixUBERON:000045894.31gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.24gold quality
ovaryUBERON:000099294.24gold quality
ectocervixUBERON:001224994.24gold quality
minor salivary glandUBERON:000183094.17gold quality
mucosa of transverse colonUBERON:000499193.98gold quality
islet of LangerhansUBERON:000000693.96gold quality
muscle layer of sigmoid colonUBERON:003580593.88gold quality
left uterine tubeUBERON:000130393.82gold quality
cerebellar hemisphereUBERON:000224593.82gold quality
cerebellar cortexUBERON:000212993.77gold quality
right hemisphere of cerebellumUBERON:001489093.66gold quality
skin of abdomenUBERON:000141693.61gold quality
smooth muscle tissueUBERON:000113593.52gold quality
body of pancreasUBERON:000115093.51gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-114yes6.93
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR, DNMT3A, DNMT3B, EPAS1, HIF1A, HOXB7, HOXD8, MBD2, MEF2D, MYT1, NFATC2, NFKB, NR2E1, RARG, RCOR2, RELA, SNAI1, TAL1, TCF12, TCF3, TET1, TP53

miRNA regulators (miRDB)

21 targeting KDM1A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-806399.9169.763146
HSA-MIR-137-3P99.8774.742401
HSA-MIR-469899.8471.414303
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-426999.5569.891373
HSA-MIR-513C-5P99.5068.421730
HSA-MIR-514B-5P99.5068.191766
HSA-MIR-372-5P99.4169.112299
HSA-MIR-371A-5P99.0866.511914
HSA-MIR-942-3P98.8169.04876
HSA-MIR-429798.7766.952013
HSA-MIR-6771-3P98.2066.53971
HSA-MIR-4797-3P97.4867.14989
HSA-MIR-194-3P97.3665.961027
HSA-MIR-444897.0466.22752
HSA-MIR-426496.3564.761480

Literature-anchored findings (GeneRIF, showing 40)

  • results thus identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histone methylases and demethylases (PMID:15620353)
  • in vivo LSD1 might not necessarily function as an oxidase, but it might use alternative electron acceptors (PMID:15811342)
  • nucleosomal demethylation is the result of CoREST enhancing the association between BHC110 and nucleosomes (PMID:16079794)
  • LSD1 interacts with androgen receptor in vitro and in vivo, and stimulates androgen-receptor-dependent transcription (PMID:16079795)
  • Results suggest that LSD1-mediated histone demethylation is regulated dynamically in vivo, and may have profound effects on gene expression under both physiological and pathological conditions. (PMID:16140033)
  • LSD1 is a chromatin-modifying enzyme, which is able to read different epigenetic marks on the histone N-terminal tail and can serve as a docking module for the stabilization of the associated corepressor complex(es) on chromatin (PMID:16223729)
  • Crystal structure of LSD1 at 2.9-A resolution. LSD1 forms a highly asymmetric, closely packed domain structure from which a long helical ’tower’ domain protrudes. (PMID:16799558)
  • The shape and dimension of LSD1-CoREST crystal structure suggest its bivalent binding to nucleosomes, allowing efficient H3-K4 demethylation. (PMID:16885027)
  • These studies reveal an intimate link between the histone demethylase and deacetylase enzymes but also identify histone demethylation as a secondary target of Histone deacetylase (HDAC) inhibitors. (PMID:16914725)
  • Results describe the 2.8-A-resolution crystal structure of the human lysine-specific demethylase 1 (LSD1) and suggest that LSD1 defines a new subfamily of FAD-dependent oxidases. (PMID:16956976)
  • Epigenetic modifications on histone H3 need to be removed before Lys4 demethylation can efficiently occur. (PMID:16987819)
  • Data suggest that LSD1 may serve as novel biomarker predictive for prostate cancer with aggressive biology and point to a role of LSD1 in constitutive activation of AR-mediated growth signals. (PMID:17145880)
  • JMJD2C and LSD1 interact and both demethylases cooperatively stimulate androgen receptor-dependent gene transcription. (PMID:17277772)
  • Tranylcypromine is a mechanism-based inactivator of LSD1. (PMID:17367163)
  • LSD1 has a pro-oncogenic function by modulating pro-survival gene expression and p53 transcriptional activity (PMID:17409384)
  • This review underscores the involvement of the first histone demethylase, lysine-specific demethylase-1, in transcriptional regulation and describes a dynamic view of histone methylation by an array of other antagonizing histone-modifying enzymes. (PMID:17504018)
  • Pull down of spiked and endogenous LSD1 from HeLa cell nuclear extracts, set the stage for activity-based demethylase proteomics. (PMID:17511474)
  • The LSD1 active site cannot productively accommodate more than three residues on the N-terminal side of the methyllysine, explaining its histone H3-K4 specificity. (PMID:17529991)
  • findings couple the function of BHC80 to that of LSD1, and indicate that unmodified H3K4 is part of the ‘histone code’ (PMID:17687328)
  • the histone lysine-specific demethylase LSD1 interacts with p53 to repress p53-mediated transcriptional activation and to inhibit the role of p53 in promoting apoptosis (PMID:17805299)
  • represses hTERT transcription via demethylating H3-K4 in normal and cancerous cells, and together with HDACs, participates in the establishment of a stable repression state of the hTERT gene in normal or differentiated malignant cells (PMID:18197256)
  • These findings indicate that Epstein-Barr virus C promoter (Cp) is a cell cycle-regulated promoter that is under the control of Rb and the histone demethylase LSD1 in multiple latency types. (PMID:18216119)
  • LSD1 has multifaceted functions in chromatin regulation [review] (PMID:18343668)
  • LSD1 is a histone demethylase that is the prime corepressor for TLX (PMID:18391013)
  • ZNF198, through its multiple protein-protein interaction interfaces, helps to maintain the intact LSD1-CoREST-HDAC1 complex on specific, non-REST-responsive promoters and may also prevent SUMO-dependent dissociation of HDAC1 (PMID:18806873)
  • The histone lysine demethylase, LSD1, is required for these ligand-induced interactive loci to associate with distinct interchromatin granules, long thought to serve as “storage” sites for the splicing machinery (PMID:19052240)
  • Blimp-1 binding to its target sites is accompanied by LSD1 binding to those same sites and LSD1 binding correlates with histone modifications of accessible chromatin. (PMID:19124609)
  • inhibition of LSD1 reprograms the transcriptome of neuroblastoma cells and inhibits neuroblastoma xenograft growth. (PMID:19223552)
  • LSD1 may negatively regulate TAL1-mediated transcription and suggest that the dynamic regulation of TAL1-associated LSD1/HDAC1 complex may determine the onset of erythroid differentiation programs. (PMID:19497860)
  • Analysis of chromatin modification patterns shows that LSD1 are recruited to the c-myc promoter leading to appearance of repressive chromatin marks. (PMID:19522008)
  • Study reports that LSD1 is an integral component of the Mi-2/nucleosome remodeling and deacetylase (NuRD) complex and demonstrated that LSD1 inhibits the invasion of breast cancer cells in vitro. (PMID:19703393)
  • high dimethylation of histone H3 at lysine 4 expression is rare in hepatocellular carcinoma compared with other carcinomas, possibly due to complex epigenetic regulation involving LSD1 (PMID:19896696)
  • when LSD1 is inhibited by oligoamine analogues, aberrantly silenced genes are reexpressed (PMID:19934284)
  • Very high LSD1 levels oocur in estrogen receptor (ER)-negative breast tumors. LSD1 is recruited to the promoters of proliferation-associated genes like p21, ERBB2 and CCNA2. (PMID:20042638)
  • identification of genetic alterations & expression changes of LSD1, JHDM2A & GASC1 in prostate cancer (PC); as no genetic alterations & only modest expression changes were found, it is unlikely they play a major role in progression of PC (PMID:20127736)
  • This study demonistrated that the arousal of neuronal LSD1 isoforms pacemakes early neurite morphogenesis, conferring a neurospecific function to LSD1 epigenetic activity. (PMID:20164337)
  • Results suggest that LSD1 plays a role in chromosomal segregation during mitosis partially through transcriptional regulation of BUBR1 and MAD2. (PMID:20189264)
  • phosphorylation of histone H3 at threonine 6 (H3T6) by protein kinase C beta I (PKCbeta(I), also known as PRKCbeta) is the key event that prevents LSD1 from demethylating H3K4 during AR-dependent gene activation (PMID:20228790)
  • this is the first evidence that Eco1 represses transcription by interacting with histone demethylase, LSD1 to convert chromatin to inactive state. (PMID:20331966)
  • Expression profile analysis show that LSD1 may affect expression of genes involved in various chromatin-modifying pathways in cancer cells. (PMID:20333681)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriokdm1aENSDARG00000060679
mus_musculusKdm1aENSMUSG00000036940
rattus_norvegicusKdm1aENSRNOG00000022372
drosophila_melanogasterSu(var)3-3FBGN0260397
caenorhabditis_elegansspr-5WBGENE00005010
caenorhabditis_elegansWBGENE00011615

Paralogs (7): MAOB (ENSG00000069535), SMOX (ENSG00000088826), IL4I1 (ENSG00000104951), PPOX (ENSG00000143224), PAOX (ENSG00000148832), KDM1B (ENSG00000165097), MAOA (ENSG00000189221)

Protein

Protein identifiers

Lysine-specific histone demethylase 1A — O60341 (reviewed: O60341)

Alternative names: BRAF35-HDAC complex protein BHC110, Flavin-containing amine oxidase domain-containing protein 2, [histone H3]-dimethyl-L-lysine(4) FAD-dependent demethylase 1A

All UniProt accessions (21): O60341, A0A8I5KPV0, A0A8I5KQU6, A0A8I5KRB8, A0A8I5KRC9, A0A8I5KRF4, A0A8I5KRX9, A0A8I5KSH0, A0A8I5KSI8, A0A8I5KT29, A0A8I5KTR5, A0A8I5KUU0, A0A8I5KV76, A0A8I5KVZ4, A0A8I5KXU4, A0A8I5QJJ5, A0A8I5QJR3, A0A8I5QJX1, A0A8I5QKM3, R4GMP9, R4GMQ1

UniProt curated annotations — full annotation on UniProt →

Function. Histone demethylase that can demethylate both ‘Lys-4’ (H3K4me) and ‘Lys-9’ (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2). May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (AR)-dependent transcription, by being recruited to AR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in AR-containing complexes, which mediates phosphorylation of ‘Thr-6’ of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated ‘Lys-370’ of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Demethylates methylated ‘Lys-42’ and methylated ‘Lys-117’ of SOX2. Required for gastrulation during embryogenesis. 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. Facilitates epithelial-to-mesenchymal transition by acting as an effector of SNAI1-mediated transcription repression of epithelial markers E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7. Required for the repression of GIPR expression. Neuron-specific histone demethylase that demethylates mono- and dimethylated ‘Lys-20’ of histone H4 (H4K20me1 and H4K20me2), a chromatin repressive mark. This demethylation is crucial for the initiation and elongation of neuronal activity-regulated genes, required for spatial learning and memory. Mediates H3K9me2 demethylation through cooperation with the supervillin protein (SVIL), and this H3K9 demethylase activity is essential for regulating gene expression during neuronal differentiation. Neuron-specific histone demethylase that demethylates mono- and dimethylated ‘Lys-20’ of histone H4 (H4K20me1 and H4K20me2), a chromatin repressive mark. This demethylation is crucial for the initiation and elongation of neuronal activity-regulated genes, required for spatial learning and memory. Mediates H3K9me2 demethylation through cooperation with the supervillin protein (SVIL), and this H3K9 demethylase activity is essential for regulating gene expression during neuronal differentiation.

Subunit / interactions. Component of a histone demethylase complex with RCOR1. Component of a RCOR/GFI/KDM1A/HDAC complex. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B, KDM1A, RCOR1 and PHF21A. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. In the complex, RCOR1/CoREST strongly enhances the demethylase activity and protects it from the proteasome while PHF21A/BHC80 inhibits the demethylase activity. Interacts with INSM1 (via N-terminus). Interacts with the androgen receptor (AR). Interacts directly with GFI1 and GFI1B. Interacts with SNAI1 (via SNAG domain). Interacts (via AOD/Tower domain) with JADE2 (via C-terminus). Interacts with ESRRB; co-occupies the core set of ESRRB targets. Interacts with SAMD1 (via WH domain); the interaction modulates KDM1A function. Interacts with RBPJ. Interacts with L3MBTL3. Interacts with ZMYND8. Interacts with FLAD1; which promotes KDM1A holoenzyme formation. Component of a histone demethylase complex with RCOR1. Forms a complex with SVIL, which functions to demethylate histone H3 at Lys-9 (H3K9me2). Component of a histone demethylase complex with RCOR1. Component of a histone demethylase complex with RCOR1. Forms a complex with SVIL, which functions to demethylate histone H3 at Lys-9 (H3K9me2).

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Ubiquitously expressed. Expressed in brain and testis. Expressed exclusively in brain tissues.

Post-translational modifications. Acetylated by KAT8 in epithelial but not in mesenchymal cells, thereby regulating the epithelial-to-mesenchymal transition. Acetylation by KAT8 reduces KDM1A association with nucleosomes, thereby decreasing histone H3 demethylation, leading to transcription activation of target genes. Polyubiquitinated by JADE2; which leads to its proteasomal degradation. Deubiquitinated by USP38; preventing it from degradation by the 26S proteasome. Phosphorylation at Thr-371 reduces interaction with corepressors, including HDAC1/2 and CoREST, thereby converting isoform 4 from a transient dominant-negative repressor of neuronal differentiation into an active isoform that promotes neural morphogenesis and maturation.

Disease relevance. Cleft palate, psychomotor retardation, and distinctive facial features (CPRF) [MIM:616728] A syndrome characterized by cleft palate, developmental delay, psychomotor retardation, and facial dysmorphic features including a prominent forehead, slightly arched eyebrows, elongated palpebral fissures, a wide nasal bridge, thin lips, and widely spaced teeth. Cleft palate is a congenital fissure of the soft and/or hard palate, due to faulty fusion. The disease is caused by variants affecting the gene represented in this entry. ACTH-independent macronodular adrenal hyperplasia 3 (AIMAH3) [MIM:620990] A form of macronodular adrenal hyperplasia, a rare adrenal defect characterized by multiple, bilateral, non-pigmented, benign, adrenocortical nodules. It results in excessive production of cortisol leading to ACTH-independent Cushing syndrome. Clinical manifestations of Cushing syndrome include facial and truncal obesity, abdominal striae, muscular weakness, osteoporosis, arterial hypertension, diabetes. AIMAH3 affected individuals have low fasting cortisol and ACTH, but excess cortisol is secreted after eating. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. The N-terminal sequences of INSM1 and SNAI1 compete with histone H3 for the same binding site and thereby inhibit histone demethylation (in vitro).

Domain organisation. The SWIRM domain may act as an anchor site for a histone tail.

Induction. Down-regulated during neural differentiation in neuroblastoma cancer.

Similarity. Belongs to the flavin monoamine oxidase family.

Isoforms (4)

UniProt IDNamesCanonical?
O60341-11, Lsd1cyes
O60341-22, 2a/8a, neuroLSD1, LSD1+2a+8a
O60341-33, 2a, LSD1+2a
O60341-44, 8a, neuroLSD1, LSD1+8a

RefSeq proteins (5): NP_001009999, NP_001350583, NP_001397691, NP_001397692, NP_055828 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002937Amino_oxidaseDomain
IPR007526SWIRMDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017366Hist_Lys-spec_deMeaseFamily
IPR036188FAD/NAD-bd_sfHomologous_superfamily
IPR036388WH-like_DNA-bd_sfHomologous_superfamily
IPR050281Flavin_monoamine_oxidaseFamily

Pfam: PF01593, PF04433

Enzyme classification (BRENDA):

  • EC 1.14.11.65 — [histone H3]-dimethyl-L-lysine9 demethylase (BRENDA: 9 organisms, 67 substrates, 84 inhibitors, 4 Km, 4 kcat entries)
  • EC 1.14.11.66 — [histone H3]-trimethyl-L-lysine9 demethylase (BRENDA: 7 organisms, 79 substrates, 168 inhibitors, 23 Km, 14 kcat entries)
  • EC 1.14.11.67 — [histone H3]-trimethyl-L-lysine4 demethylase (BRENDA: 13 organisms, 78 substrates, 122 inhibitors, 22 Km, 20 kcat entries)
  • EC 1.14.99.66 — [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase (BRENDA: 5 organisms, 74 substrates, 154 inhibitors, 30 Km, 25 kcat entries)

Substrate kinetics (BRENDA)

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

SubstrateKm (mM)Measurements
H3K4ME2 1-21 PEPTIDE0.0045–0.0356
HISTONE H3 N6,N6,N6-TRIMETHYL-L-LYSINE90.023–0.0485
HISTONE H3 N6,N6-DIMETHYL-L-LYSINE90.025–0.0745
[HISTONE H3]-N6,N6-L-DIMETHYLLYSINE4-1-210.0045–0.00893
[HISTONE H3]-N6,N6-DIMETHYL-L-LYSINE90.106–0.10612
[HISTONE H3]-N6-METHYL-L-LYSINE90.095–0.09522
2-OXOGLUTARATE0.02472
H31-15K9ME30.02322
O20.1732
[ACETYLATED HISTONE H3 21MER]-N6,N6,N6-TRIMETHYL0.0168–0.09552
[ACETYLATED HISTONE H3 21MER]-N6,N6-DIMETHYL-L-L0.0547–0.2292
[HISTONE H3]-N6,N6-DIMETHYL-L-LYSINE40.0107–0.01282
[HISTONE H3 PEPTIDE 21MER]-N6-METHYL-L-LYSINE40.0113–0.0922
[HISTONE H3, A7H]-N6,N6,N6-TRIMETHYL-L-LYSINE 90.111
[HISTONE H3, A7R]-N6,N6,N6-TRIMETHYL-L-LYSINE 90.181

Catalyzed reactions (Rhea), 8 shown:

  • N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + 2 2-oxoglutarate + 2 O2 = L-lysyl(9)-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2 (RHEA:60188)
  • N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + 2-oxoglutarate + O2 = N(6)-methyl-L-lysyl(9)-[histone H3] + formaldehyde + succinate + CO2 (RHEA:60192)
  • N(6)-methyl-L-lysyl(9)-[histone H3] + 2-oxoglutarate + O2 = L-lysyl(9)-[histone H3] + formaldehyde + succinate + CO2 (RHEA:60196)
  • N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + 2 A + 2 H2O = L-lysyl(4)-[histone H3] + 2 formaldehyde + 2 AH2 (RHEA:60244)
  • N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + A + H2O = N(6)-methyl-L-lysyl(4)-[histone H3] + formaldehyde + AH2 (RHEA:60248)
  • N(6)-methyl-L-lysyl(4)-[histone H3] + A + H2O = L-lysyl(4)-[histone H3] + formaldehyde + AH2 (RHEA:60256)
  • N(6)-methyl-L-lysyl(20)-[histone H4] + 2-oxoglutarate + O2 = L-lysyl(20)-[histone H4] + formaldehyde + succinate + CO2 (RHEA:67804)
  • N(6),N(6)-dimethyl-L-lysyl(20)-[histone H4] + 2-oxoglutarate + O2 = N(6)-methyl-L-lysyl(20)-[histone H4] + formaldehyde + succinate + CO2 (RHEA:85907)

UniProt features (131 total): strand 34, helix 28, sequence variant 15, modified residue 13, turn 8, mutagenesis site 8, binding site 7, sequence conflict 4, cross-link 3, compositionally biased region 3, region of interest 2, splice variant 2, coiled-coil region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

128 structures, top 30 by resolution.

PDBMethodResolution (Å)
6E1FX-RAY DIFFRACTION1.16
5IT3X-RAY DIFFRACTION1.4
5AFWX-RAY DIFFRACTION1.6
7JK7X-RAY DIFFRACTION1.96
7JJMX-RAY DIFFRACTION2.06
2Z3YX-RAY DIFFRACTION2.25
2Z5UX-RAY DIFFRACTION2.25
6KGOX-RAY DIFFRACTION2.25
6KGPX-RAY DIFFRACTION2.25
7E0GX-RAY DIFFRACTION2.25
7XW8X-RAY DIFFRACTION2.28
2DW4X-RAY DIFFRACTION2.3
6KGQX-RAY DIFFRACTION2.32
6KGRX-RAY DIFFRACTION2.32
7W3LX-RAY DIFFRACTION2.51
5H6QX-RAY DIFFRACTION2.53
2IW5X-RAY DIFFRACTION2.57
5H6RX-RAY DIFFRACTION2.6
5L3DX-RAY DIFFRACTION2.6
6TUYX-RAY DIFFRACTION2.6
7JJLX-RAY DIFFRACTION2.6
8Q1GX-RAY DIFFRACTION2.6
6KGMX-RAY DIFFRACTION2.62
6KGNX-RAY DIFFRACTION2.62
8INLX-RAY DIFFRACTION2.62
7CDCX-RAY DIFFRACTION2.64
9DBPX-RAY DIFFRACTION2.66
7CDEX-RAY DIFFRACTION2.68
7CDFX-RAY DIFFRACTION2.68
5X60X-RAY DIFFRACTION2.69

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O60341-F185.290.78

Functional residue map

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

Ligand- & substrate-binding residues (7): 308; 310; 316; 332–333; 801; 810–811; 289

Post-translational modifications (16): 371, 59, 104, 126, 131, 135, 137, 166, 432, 433, 436, 611, 849, 442, 469, 503

Mutagenesis-validated functional residues (8):

PositionPhenotype
685abolishes histone h4k20 demethylase activity.
432–436mimics acetylation; preventing association with chromatin.
432–436abolished acetylation by kat8, promoting association with chromatin.
503loss of polyubiquitination.
535strongly reduces demethylase activity.
564strongly reduces demethylase activity.
661abolishes histone demethylase activity.
761strongly reduces demethylase activity.

Function

Pathways and Gene Ontology

Reactome pathways

27 pathways

IDPathway
R-HSA-3214815HDACs deacetylate histones
R-HSA-3214842HDMs demethylate histones
R-HSA-5625886Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-8943724Regulation of PTEN gene transcription
R-HSA-9018519Estrogen-dependent gene expression
R-HSA-9029569NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux
R-HSA-9679191Potential therapeutics for SARS
R-HSA-9764725Negative Regulation of CDH1 Gene Transcription
R-HSA-983231Factors involved in megakaryocyte development and platelet production
R-HSA-109582Hemostasis
R-HSA-1257604PIP3 activates AKT signaling
R-HSA-162582Signal Transduction
R-HSA-1643685Disease
R-HSA-194315Signaling by Rho GTPases
R-HSA-195258RHO GTPase Effectors
R-HSA-3247509Chromatin modifying enzymes
R-HSA-4839726Chromatin organization
R-HSA-5625740RHO GTPases activate PKNs
R-HSA-5663205Infectious disease
R-HSA-6807070PTEN Regulation
R-HSA-8939211ESR-mediated signaling
R-HSA-9006925Intracellular signaling by second messengers
R-HSA-9006931Signaling by Nuclear Receptors
R-HSA-9024446NR1H2 and NR1H3-mediated signaling
R-HSA-9679506SARS-CoV Infections
R-HSA-9716542Signaling by Rho GTPases, Miro GTPases and RHOBTB3
R-HSA-9824446Viral Infection Pathways

MSigDB gene sets: 635 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_REGULATION_OF_DNA_RECOMBINATION, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_RESPONSE_TO_IONIZING_RADIATION, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE_BY_P53_CLASS_MEDIATOR, GOBP_NEGATIVE_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_BY_P53_CLASS_MEDIATOR, GOBP_CELLULAR_RESPONSE_TO_UV, GOBP_POSITIVE_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_NEURON_MATURATION, GOBP_CELLULAR_RESPONSE_TO_LIGHT_STIMULUS, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MODULE_493

GO Biological Process (37): negative regulation of transcription by RNA polymerase II (GO:0000122), positive regulation of neuroblast proliferation (GO:0002052), regulation of transcription by RNA polymerase II (GO:0006357), regulation of double-strand break repair via homologous recombination (GO:0010569), positive regulation of epithelial to mesenchymal transition (GO:0010718), positive regulation of neuron projection development (GO:0010976), cerebral cortex development (GO:0021987), positive regulation of protein ubiquitination (GO:0031398), regulation of protein localization (GO:0032880), cellular response to UV (GO:0034644), epigenetic regulation of gene expression (GO:0040029), neuron maturation (GO:0042551), negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518), positive regulation of cell size (GO:0045793), positive regulation of transcription by RNA polymerase II (GO:0045944), guanine metabolic process (GO:0046098), muscle cell development (GO:0055001), regulation of androgen receptor signaling pathway (GO:0060765), response to fungicide (GO:0060992), cellular response to cAMP (GO:0071320), cellular response to gamma radiation (GO:0071480), positive regulation of cold-induced thermogenesis (GO:0120162), DNA repair-dependent chromatin remodeling (GO:0140861), negative regulation of transcription initiation-coupled chromatin remodeling (GO:0160217), negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166), negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254), positive regulation of neural precursor cell proliferation (GO:2000179), positive regulation of stem cell proliferation (GO:2000648), epithelial to mesenchymal transition (GO:0001837), chromatin organization (GO:0006325), chromatin remodeling (GO:0006338), regulation of DNA-templated transcription (GO:0006355), regulation of gene expression (GO:0010468), negative regulation of macromolecule biosynthetic process (GO:0010558), positive regulation of cell differentiation (GO:0045597), regulation of neurogenesis (GO:0050767), positive regulation of multicellular organismal process (GO:0051240)

GO Molecular Function (22): p53 binding (GO:0002039), chromatin binding (GO:0003682), transcription coactivator activity (GO:0003713), transcription corepressor activity (GO:0003714), oxidoreductase activity (GO:0016491), enzyme binding (GO:0019899), histone demethylase activity (GO:0032452), histone H3K4 demethylase activity (GO:0032453), histone H3K9 demethylase activity (GO:0032454), histone H4K20 demethylase activity (GO:0035575), identical protein binding (GO:0042802), MRF binding (GO:0043426), flavin adenine dinucleotide binding (GO:0050660), nuclear androgen receptor binding (GO:0050681), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), telomeric repeat-containing RNA binding (GO:0061752), DNA-binding transcription factor binding (GO:0140297), protein demethylase activity (GO:0140457), FAD-dependent H3K4me/H3K4me3 demethylase activity (GO:0140682), promoter-specific chromatin binding (GO:1990841), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (9): chromosome, telomeric region (GO:0000781), chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription regulator complex (GO:0005667), protein-containing complex (GO:0032991), histone methyltransferase complex (GO:0035097), DNA repair complex (GO:1990391), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-15 pathways:

CategoryPathways
Chromatin modifying enzymes2
RHO GTPases activate PKNs1
PTEN Regulation1
ESR-mediated signaling1
NR1H2 and NR1H3-mediated signaling1
SARS-CoV Infections1
Regulation of CDH1 Gene Transcription1
Hemostasis1
Intracellular signaling by second messengers1
Signaling by Rho GTPases, Miro GTPases and RHOBTB31
Signaling by Rho GTPases1
Chromatin organization1
RHO GTPase Effectors1
Disease1
PIP3 activates AKT signaling1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transcription by RNA polymerase II3
protein binding3
regulation of transcription by RNA polymerase II2
negative regulation of DNA-templated transcription2
positive regulation of DNA-templated transcription2
transcription coregulator activity2
histone H3 demethylase activity2
cellular anatomical structure2
neuroblast proliferation1
positive regulation of neurogenesis1
regulation of neuroblast proliferation1
positive regulation of neural precursor cell proliferation1
regulation of DNA-templated transcription1
regulation of DNA recombination1
double-strand break repair via homologous recombination1
regulation of double-strand break repair1
epithelial to mesenchymal transition1
regulation of epithelial to mesenchymal transition1
positive regulation of cell differentiation1
positive regulation of multicellular organismal process1
regulation of neuron projection development1
neuron projection development1
positive regulation of cell projection organization1
pallium development1
anatomical structure development1
protein ubiquitination1
regulation of protein ubiquitination1
positive regulation of protein modification by small protein conjugation or removal1
intracellular protein localization1
regulation of localization1
response to UV1
cellular response to light stimulus1
chromatin remodeling1
regulation of gene expression1
cell maturation1
neuron development1
DNA damage response, signal transduction by p53 class mediator1
regulation of DNA damage response, signal transduction by p53 class mediator1
negative regulation of signal transduction by p53 class mediator1
regulation of cell size1

Protein interactions and networks

STRING

4241 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KDM1ARCOR1Q9UKL0999
KDM1AHDAC1Q13547998
KDM1AHDAC2Q92769997
KDM1ADNMT1P26358996
KDM1AEZH2Q15910994
KDM1ACTBP1Q13363993
KDM1APHF21AQ96BD5993
KDM1AEHMT2Q96KQ7989
KDM1ASNAI1O95863986
KDM1AKDM5BQ9UGL1983
KDM1AGFI1Q99684982
KDM1AARP10275982
KDM1ARESTQ13127978
KDM1AHMG20BQ9P0W2976
KDM1ACHD4Q14839972

IntAct

667 interactions, top by confidence:

ABTypeScore
KDM1ARCOR1psi-mi:“MI:0407”(direct interaction)0.900
CTBP1KDM1Apsi-mi:“MI:0914”(association)0.790
HMG20AKDM1Apsi-mi:“MI:0914”(association)0.730
KDM1Apsi-mi:“MI:0915”(physical association)0.700
NR2E1KDM1Apsi-mi:“MI:0914”(association)0.680
NR2E1KDM1Apsi-mi:“MI:2364”(proximity)0.680
KDM1AMYCpsi-mi:“MI:0915”(physical association)0.670
KDM1ATMEM266psi-mi:“MI:0915”(physical association)0.670
KDM1AZBED1psi-mi:“MI:0915”(physical association)0.670
KDM1ATRAF4psi-mi:“MI:0915”(physical association)0.670
KDM1AKRT33Bpsi-mi:“MI:0915”(physical association)0.670
KDM1ASPICE1psi-mi:“MI:0915”(physical association)0.670
KDM1ARBPJpsi-mi:“MI:0915”(physical association)0.640
RBPJKDM1Apsi-mi:“MI:0915”(physical association)0.640
NOTCH1KDM1Apsi-mi:“MI:0914”(association)0.560
KDM1ANOTCH1psi-mi:“MI:0914”(association)0.560
NOTCH1KDM1Apsi-mi:“MI:0915”(physical association)0.560
RCOR2KDM1Apsi-mi:“MI:0914”(association)0.560
KDM1AANKRD23psi-mi:“MI:0915”(physical association)0.560
KDM1ATNNT2psi-mi:“MI:0915”(physical association)0.560
KDM1ACEP57psi-mi:“MI:0915”(physical association)0.560
KDM1AUBASH3Bpsi-mi:“MI:0915”(physical association)0.560
KDM1ATLE5psi-mi:“MI:0915”(physical association)0.560

BioGRID (1327): KDM1A (Two-hybrid), KDM1A (Two-hybrid), KDM1A (Two-hybrid), KDM1A (Two-hybrid), CCDC53 (Two-hybrid), TRIM39 (Two-hybrid), TRIM54 (Two-hybrid), KLC3 (Two-hybrid), KDM1A (Affinity Capture-Western), USP28 (Affinity Capture-Western), USP28 (Reconstituted Complex), KDM1A (Biochemical Activity), KDM1A (Affinity Capture-MS), KDM1A (Affinity Capture-MS), KDM1A (Affinity Capture-MS)

ESM2 similar proteins: A1A4J8, A6H784, D3ZS74, D4A6D7, E9QBI7, O42899, O43819, O60341, O75880, P00258, P10109, P23833, P24483, P30048, P38072, Q05B51, Q0VCH8, Q12931, Q2KHU5, Q2NKY8, Q2TBI4, Q3ULF4, Q4VAE3, Q5EA41, Q5REY3, Q5RH02, Q5SUC9, Q69ZP3, Q6DKK2, Q6PI78, Q6ZQ88, Q7ZUC7, Q8BMS4, Q8JZQ2, Q8LAL0, Q8N490, Q8VCL2, Q920A7, Q95N00, Q96HS1

Diamond homologs: A0A024BTN9, A0A2U8QPE6, A2XDA1, A6MFL0, A8QL51, A8QL52, A8QL58, B0VXW0, B3EWI9, B5AR80, B5U6Y8, C0HJE7, F8S0Z5, G8XQX1, J7H670, K9N7B7, O08615, O09046, O24164, O34363, O60341, O93364, P0C2D1, P0C2D2, P0C2D3, P0C2D4, P0C2D5, P0C2D6, P0C2D7, P0CC17, P0CJ40, P0DI84, P0DI87, P0DI88, P0DI89, P0DI91, P0DPS2, P0DQH9, P0DV78, P28553

SIGNOR signaling

23 interactions.

AEffectBMechanism
KDM1A“form complex”“CoREST-HDAC complex”binding
KDM4C“up-regulates activity”KDM1Abinding
KDM1A“form complex”“BHC complex”binding
KDM1A“up-regulates activity”H3C1demethylation
KDM1A“up-regulates activity”H3-4demethylation
KDM1A“up-regulates activity”H3-3Ademethylation
KDM1A“up-regulates activity”“Histone H3”demethylation
BRMS1“up-regulates activity”KDM1Abinding
ASXL3“down-regulates activity”KDM1Abinding
GTF2I“up-regulates activity”KDM1Abinding
GTF2I“up-regulates activity”KDM1Arelocalization
KDM1Adown-regulatesEpigenetic_regulation
HIF1A“down-regulates quantity by repression”KDM1A“transcriptional regulation”
EPAS1“down-regulates quantity by repression”KDM1A“transcriptional regulation”
CSNK2A1“up-regulates activity”KDM1Aphosphorylation
PPM1D“down-regulates activity”KDM1Adephosphorylation
GSK3B“up-regulates activity”KDM1Aphosphorylation
PRKCQ“down-regulates activity”KDM1Aphosphorylation
PRKCA“up-regulates activity”KDM1Aphosphorylation
PHF21A“down-regulates activity”KDM1Abinding
RCOR1“up-regulates activity”KDM1Abinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 113 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:

PathwayPartnersFoldFDR
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)918.6×5e-07
NOTCH1 Intracellular Domain Regulates Transcription516.8×6e-04
Regulation of PTEN gene transcription615.1×2e-04
Constitutive Signaling by NOTCH1 PEST Domain Mutants513.9×9e-04
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants513.9×9e-04
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression612.9×4e-04
Formation of the beta-catenin:TCF transactivating complex711.8×2e-04
HDACs deacetylate histones711.8×2e-04

GO biological processes:

GO termPartnersFoldFDR
morphogenesis of an epithelium620.8×1e-04
outflow tract morphogenesis515.5×2e-03
intermediate filament organization614.6×6e-04
circadian regulation of gene expression511.8×5e-03
epithelial cell differentiation610.6×2e-03
chromatin remodeling107.4×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

1163 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic7
Likely pathogenic9
Uncertain significance616
Likely benign454
Benign25

Top pathogenic / likely-pathogenic (16)

Variant IDHGVSClassification
218911NM_001009999.3(KDM1A):c.2353T>C (p.Tyr785His)Pathogenic
218912NM_001009999.3(KDM1A):c.1207G>A (p.Glu403Lys)Pathogenic
218913NM_001009999.3(KDM1A):c.1739A>G (p.Asp580Gly)Pathogenic
3366856NM_001009999.3(KDM1A):c.1849dup (p.Val617fs)Pathogenic
3366857NM_001009999.3(KDM1A):c.352-1G>APathogenic
3366858NM_001009999.3(KDM1A):c.811C>T (p.Arg271Ter)Pathogenic
3366859NM_001009999.3(KDM1A):c.1984C>T (p.Gln662Ter)Pathogenic
1516162NM_001009999.3(KDM1A):c.1736A>G (p.Asp579Gly)Likely pathogenic
1691768NM_001009999.3(KDM1A):c.1208A>C (p.Glu403Ala)Likely pathogenic
1697992NM_001009999.3(KDM1A):c.1736A>T (p.Asp579Val)Likely pathogenic
1700098NM_001009999.3(KDM1A):c.1733A>G (p.Gln578Arg)Likely pathogenic
3910195NM_001009999.3(KDM1A):c.1035_1038dup (p.Ala347fs)Likely pathogenic
3910225NM_001009999.3(KDM1A):c.2299-2A>CLikely pathogenic
4277973NM_001009999.3(KDM1A):c.532C>T (p.Leu178Phe)Likely pathogenic
451410NM_001009999.3(KDM1A):c.1196A>G (p.Asp399Gly)Likely pathogenic
559560NM_001009999.3(KDM1A):c.1003G>T (p.Gly335Ter)Likely pathogenic

SpliceAI

2745 predictions. Top by Δscore:

VariantEffectΔscore
1:23019945:AAGGT:Adonor_loss1.0000
1:23019946:AGG:Adonor_loss1.0000
1:23019947:GGTA:Gdonor_loss1.0000
1:23019948:G:GAdonor_loss1.0000
1:23019949:T:Gdonor_loss1.0000
1:23030635:G:Tdonor_loss1.0000
1:23030636:T:Gdonor_loss1.0000
1:23050516:GCACA:Gdonor_gain1.0000
1:23050517:CACA:Cdonor_gain1.0000
1:23050518:ACA:Adonor_gain1.0000
1:23050519:CA:Cdonor_gain1.0000
1:23050520:AG:Adonor_loss1.0000
1:23050521:G:GGdonor_gain1.0000
1:23050522:TAA:Tdonor_loss1.0000
1:23053759:A:AGacceptor_gain1.0000
1:23053760:G:GGacceptor_gain1.0000
1:23053840:G:GGdonor_gain1.0000
1:23055145:GA:Gdonor_gain1.0000
1:23055162:G:GGdonor_gain1.0000
1:23055204:T:Gdonor_gain1.0000
1:23055930:A:AGacceptor_gain1.0000
1:23055931:G:GAacceptor_gain1.0000
1:23056037:GG:Gdonor_gain1.0000
1:23056038:GG:Gdonor_gain1.0000
1:23057476:T:TAacceptor_gain1.0000
1:23057483:GGATC:Gacceptor_gain1.0000
1:23057552:G:GAdonor_gain1.0000
1:23057561:TCTTG:Tdonor_gain1.0000
1:23057563:TTGG:Tdonor_loss1.0000
1:23057564:TG:Tdonor_gain1.0000

AlphaMissense

5680 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:23050402:C:AA178D1.000
1:23050404:T:CF179L1.000
1:23050406:C:AF179L1.000
1:23050406:C:GF179L1.000
1:23050410:A:CS181R1.000
1:23050412:C:AS181R1.000
1:23050412:C:GS181R1.000
1:23050417:T:CL183P1.000
1:23050432:T:GM188R1.000
1:23050443:G:AE192K1.000
1:23050444:A:TE192V1.000
1:23050445:A:CE192D1.000
1:23050445:A:TE192D1.000
1:23050446:G:CA193P1.000
1:23050456:T:CF196S1.000
1:23050509:A:GR214G1.000
1:23050510:G:CR214T1.000
1:23050510:G:TR214I1.000
1:23050511:A:CR214S1.000
1:23050511:A:TR214S1.000
1:23050514:C:AN215K1.000
1:23050514:C:GN215K1.000
1:23050516:G:CR216P1.000
1:23053762:T:CL218P1.000
1:23053770:T:AW221R1.000
1:23053770:T:CW221R1.000
1:23055090:G:CR251P1.000
1:23055111:G:CR258P1.000
1:23055127:C:AN263K1.000
1:23055127:C:GN263K1.000

dbSNP variants (sampled 300 via entrez): RS1000019170 (1:23038723 A>C,G), RS1000026842 (1:23025364 CTT>C), RS1000083766 (1:23077594 T>C), RS1000088818 (1:23029043 T>G), RS1000141130 (1:23028689 C>G), RS1000207597 (1:23059385 T>C), RS1000251175 (1:23036080 T>G), RS1000369644 (1:23019054 G>A), RS1000390157 (1:23056185 A>G), RS1000416720 (1:23079188 C>G), RS1000471412 (1:23070363 C>T), RS1000498286 (1:23050988 A>G), RS1000526431 (1:23078419 C>T), RS1000704929 (1:23035765 T>C), RS1000708717 (1:23058185 C>T)

Disease associations

OMIM: gene MIM:609132 | disease phenotypes: MIM:616728, MIM:620990

GenCC curated gene-disease

DiseaseClassificationInheritance
palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndromeStrongAutosomal dominant

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndromeDefinitiveAD

Mondo (4): palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome (MONDO:0014751), ACTH-independent macronodular adrenal hyperplasia 3 (MONDO:0700299), coloboma (MONDO:0001476), intellectual disability (MONDO:0001071)

Orphanet (3): Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome (Orphanet:477993), OBSOLETE: Ocular coloboma (Orphanet:194), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

98 total (30 of 98 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000028Cryptorchidism
HP:0000041Chordee
HP:0000047Hypospadias
HP:0000174Abnormal palate morphology
HP:0000219Thin upper lip vermilion
HP:0000248Brachycephaly
HP:0000256Macrocephaly
HP:0000316Hypertelorism
HP:0000431Wide nasal bridge
HP:0000463Anteverted nares
HP:0000486Strabismus
HP:0000494Downslanted palpebral fissures
HP:0000508Ptosis
HP:0000577Exotropia
HP:0000592Blue sclerae
HP:0000657Oculomotor apraxia
HP:0000664Synophrys
HP:0000687Widely spaced teeth
HP:0000712Emotional lability
HP:0000716Depression
HP:0000725Psychotic episodes
HP:0000750Delayed speech and language development
HP:0000787Nephrolithiasis
HP:0000822Hypertension
HP:0000858Irregular menstruation
HP:0000859Increased circulating aldosterone concentration
HP:0000939Osteoporosis
HP:0000978Bruising susceptibility
HP:0000998Hypertrichosis

GWAS associations

12 associations (top):

StudyTraitp-value
GCST005905_12Global electrical heterogeneity phenotypes3.000000e-09
GCST006019_19Gamma glutamyl transferase levels6.000000e-14
GCST007096_147Pulse pressure1.000000e-08
GCST010696_9Cortical thickness (min-P)3.000000e-08
GCST010697_34Cortical surface area (min-P)5.000000e-08
GCST010698_71Subcortical volume (min-P)4.000000e-14
GCST010699_32Brain morphology (min-P)6.000000e-09
GCST010700_65Cortical thickness (MOSTest)3.000000e-09
GCST010701_93Cortical surface area (MOSTest)2.000000e-13
GCST010702_34Subcortical volume (MOSTest)1.000000e-10
GCST010703_189Brain morphology (MOSTest)7.000000e-11
GCST011349_34Gamma glutamyl transferase levels2.000000e-12

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004327electrocardiography
EFO:0004532serum gamma-glutamyl transferase measurement
EFO:0005763pulse pressure measurement
EFO:0004346neuroimaging measurement
EFO:0004840cortical thickness

MeSH disease descriptors (2)

DescriptorNameTree numbers
D003103ColobomaC11.250.110; C11.270.147; C16.131.384.282
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (7): CHEMBL3137262 (PROTEIN COMPLEX), CHEMBL4296114 (PROTEIN COMPLEX), CHEMBL5169078 (PROTEIN-PROTEIN INTERACTION), CHEMBL5483007 (PROTEIN-PROTEIN INTERACTION), CHEMBL5483008 (PROTEIN-PROTEIN INTERACTION), CHEMBL6136 (SINGLE PROTEIN), CHEMBL6195588 (PROTEIN-PROTEIN INTERACTION)

Molecules with ChEMBL bioactivity

38 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 997,453 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL3353410OSIMERTINIB48,898
CHEMBL3989843TRANYLCYPROMINE470
CHEMBL6067481COLISTIN4
CHEMBL1089PHENELZINE418,793
CHEMBL231884DIOSMIN44,880
CHEMBL294199CAPSAICIN452,939
CHEMBL295124BERBERINE426,682
CHEMBL428647PACLITAXEL4332,542
CHEMBL43AMSACRINE482,326
CHEMBL553ERLOTINIB4108,300
CHEMBL564PROMAZINE49,707
CHEMBL588FENOLDOPAM46,729
CHEMBL71CHLORPROMAZINE445,827
CHEMBL81RALOXIFENE478,049
CHEMBL140CURCUMIN393,882
CHEMBL165RESVERATROL360,144
CHEMBL1697766PERAZINE32,664
CHEMBL226335RUTIN357,988
CHEMBL27759ENTINOSTAT36,584
CHEMBL4297289BOMEDEMSTAT3449
CHEMBL449317HESPERIDIN3
CHEMBL498485ICARITIN3
CHEMBL50QUERCETIN3
CHEMBL553204ICARIIN3
CHEMBL3781751IADADEMSTAT2
CHEMBL2106299FENETHAZINE2
CHEMBL250450ISOQUERCETIN2
CHEMBL4283683DOMATINOSTAT2
CHEMBL4297641SECLIDEMSTAT2
CHEMBL444478ACETOSIDE2

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

GtoPdb / IUPHAR curated pharmacology

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

Target class: enzyme — 1.14.11.- Histone demethylases

Most potent curated ligand interactions (10 total), top 10:

LigandActionAffinityParameter
CC-90011Inhibition9.52pIC50
TAK-418Inhibition8.54pIC50
GSK-LSD1Inhibition7.8pIC50
OG-L002Inhibition7.7pIC50
ORY-1001Activation7.7pIC50
RN-1Inhibition7.0pIC50
salvianolic acid BInhibition6.96pIC50
GSK2879552Inhibition6.4pIC50
NCL-1Inhibition5.8pIC50
tranylcypromineInhibition4.4pIC50

Binding affinities (BindingDB)

1207 measured of 2592 human assays (2594 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
(E)-3-(4- (((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5-(6,7- difluoro-1-(2-hydroxy- 2-methylpropyl)-1H- benzo[d][1,2,3]triazol- 5-yl)pyridin-2- yl)piperidin-4- yl)amino)methyl) phenyl- N-hydroxyacrylamide formateIC500.02 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
3-(3-chloro-4-((1-(3- cyano-4-(4-cyano-3- fluorophenyl)-5-(3- hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl) phenyl)- N- hydroxypropanamide formateIC500.03 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(4- (((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5-(3- hydroxy- 4-(2-hydroxy- 2- methylpropoxy) phenyl) pyridin-2- yl)piperidin- 4- yl)amino)methyl) phenyl)- N-hydroxybut-2- enamide hydrochlorideIC500.04 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
7-(4-(6-(4-aminopiperidin-1-yl)-2-(4-cyano-3-fluorophenyl)-4-methoxypyridin-3-yl)-2-hydroxyphenoxy)-N-hydroxyheptanamide hydrochlorideIC500.05 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-(2-fluoro-4-methylphenyl)phenyl]-2-fluorobenzonitrileIC500.062 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
(E)-3-(4-(2-(4-(6-(4-Aminopiperidin-1-yl)-5-cyano-4-(4-cyano-3-fluorophenyl)pyridin-3-yl)-2-hydroxyphenoxy)ethyl)phenyl)-N-hydroxyacrylamideIC500.07 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-[7-chloro-1-(2-ethyl-2-hydroxybutyl)-6-fluorobenzotriazol-5-yl]phenyl]-2-fluorobenzonitrileIC500.075 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-[1-(2-ethyl-2-hydroxybutyl)-6,7-difluorobenzotriazol-5-yl]phenyl]-2-fluorobenzonitrileIC500.076 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
(E)-3-(5- (((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5-(1H- indazol-6-yl) pyridin-2- yl)piperidin-4- yl)amino)methyl) pyridin-2-yl)-N- hydroxyacrylamide formateIC500.09 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
2-(4-(((1-(3- Cyano-4- (4-cyano-3- fluorophenyl)-5-(3- hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl) phenoxy)-N- hydroxypropanamide formateIC500.09 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(5- ((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5-(1H- indazol-6- yl)pyridin-2- yl)piperidin-4- yl)amino)methyl) pyrimidin-2-yl)-N- hydroxyacrylamide formateIC500.09 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-[6,7-difluoro-1-(2-hydroxy-2-methylpropyl)benzotriazol-5-yl]phenyl]-2-fluorobenzonitrileIC500.091 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-[6-fluoro-1-(2-hydroxy-2-methylpropyl)indazol-5-yl]phenyl]-2-fluorobenzonitrileIC500.1 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
N1-(4-(6-(4-aminopiperidin-1-yl)-5-cyano-4-(4-cyano-3-fluorophenyl)pyridin-3-yl)-2-hydroxyphenyl)-N8-hydroxyoctanediamide hydrochlorideIC500.1 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(4-(((1-(3- Cyano-4-(4- cyano-3- fluorophenyl)-5- (3-hydroxy-4-(2- hydroxy-2- methylpropoxy) phenyl)pyridin-2- yl)piperidin-4- yl)amino)methyl) phenyl)-N- hydroxyacrylamide formateIC500.1 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(4- (((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5-(3- hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl)-1H- indazol-7-yl)-N- hydroxyacrylamide formateIC500.11 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
US10723742, Example 269IC500.12 nMUS-12435128: Method for predicting therapeutic effect of LSD1 inhibitor based on expression of INSM1
7-(4-(6-(4- Aminopiperidin-1-yl)- 5-cyano-4-(4-cyano-3- fluorophenyl)-2- methylpyridin-3-yl)-2- hydroxyphenoxy)-N- hydroxyheptanamide hydrochlorideIC500.12 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
4-(((1-(3- Cyano-4-(4-cyano- 3-fluorophenyl)- 5-(3-hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl)-N- hydroxybenzamide hydrochlorideIC500.13 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(2- cyano-4-((1- (3-cyano- 4-(4-cyano-3- fluorophenyl)-5-(3- hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl) phenoxy)-N- hydroxyacetamide formateIC500.13 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
US10723742, Example 263IC500.14 nMUS-12435128: Method for predicting therapeutic effect of LSD1 inhibitor based on expression of INSM1
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-[7-bromo-6-fluoro-1-(2-hydroxy-2-methylpropyl)benzotriazol-5-yl]phenyl]-2-fluorobenzonitrileIC500.14 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-[7-bromo-1-(2-ethyl-2-hydroxybutyl)-6-fluorobenzotriazol-5-yl]phenyl]-2-fluorobenzonitrileIC500.15 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
4-((4-(4-(5-Cyano-4- (4-cyano-3-fluoro- phenyl)-6-(4- (methylamino) piperidin- 1-yl)pyridin-3-yl)-2- hydroxyphenyl) amino)methyl)-N- hydroxybenzamide hydrochlorideIC500.15 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
2-((4-((1-(3- cyano-4-(4- cyano-3- fluorophenyl)- 5-(3-hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl) phenyl) thio)-N- hydroxyacetamide formateIC500.15 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
2-(2-(1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5- (3-hydroxy-4- methoxyphenyl) pyridin-2- yl)piperidin-4- yl)amino)ethyl) amino)-N- hydroxypyrimidine- 5-carboxamide formateIC500.16 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
4-[5-(1-amino-8-azabicyclo[3.2.1]octane-8-carbonyl)-2-(6-fluoro-1-methylindol-5-yl)phenyl]-2-fluorobenzonitrileIC500.18 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-[6-fluoro-1-(2-hydroxy-2-methylpropyl)indol-5-yl]phenyl]-2-fluorobenzonitrileIC500.18 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
(E)-3-(6- (((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5-(1-(2- hydroxy-2- methylpropyl)-1H- benzo[d][1,2,3]triazol- 5-yl)pyridin-2- yl)piperidin-4- yl)amino)methyl) pyridin- 3-yl)-N- hydroxyacrylamide formateIC500.19 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
3-(4-((1- (3-Cyano-4-(4- cyano-3- fluorophenyl)- 5-(3-hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl) phenyl)- 2-fluoro-N- hydroxypropanamide formateIC500.21 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
3-(4-((1-(3- Cyano-4-(4- cyano-3-fluorophenyl)- 5-(3-hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl)-2- fluorophenyl)-N- hydroxypropanamide formateIC500.22 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
4-[5-[[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]methyl]-2-[2-fluoro-4-(2-hydroxy-2-methylpropyl)phenyl]phenyl]-2-fluorobenzonitrileIC500.23 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
(E)-3-(4-(4-(5-(4- Aminopiperidin-1-yl)- 7-(4-cyano-3- fluorophenyl)imidazo [1,2-c]pyrimidin-8-yl)- 2- hydroxyphenoxy) methyl)phenyl)-N- hydroxyacrylamide hydrochlorideIC500.23 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
7-(4-(6-(4- Aminopiperidin-1-yl)- 5-cyano-4-(4-cyano-3- fluorophenyl)pyridin-3- yl)-2-hydroxyphenoxy)- N-hydroxyheptanamide hydrochlorideIC500.23 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
N1-(4-(5-(4-aminopiperidin-1-yl)-7-(4-cyano-3-fluorophenyl)imidazo[1,2-c]pyrimidin-8-yl)-2-hydroxyphenyl)-N8-hydroxyoctanediamineIC500.26 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
US10723742, Example 125IC500.28 nMUS-12435128: Method for predicting therapeutic effect of LSD1 inhibitor based on expression of INSM1
3-(4-(((1- (3-Cyano-4- (4-cyano-3- fluorophenyl)-5-(3- hydroxy-4- (2-hydroxy- 2- methylpropoxy) phenyl) pyridin-2- yl)piperidin- 4- yl)amino)methyl) phenyl)- N- hydroxypropanamide formateIC500.3 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
7-(4-(5-(5-(5-Amino- 2-azabicyclo [2.2.1]heptan- 2-yl)-7-(4-cyano- 3- fluorophenyl)imidazo [1,2-c]pyrimidin-8-yl)- 2-hydroxyphenoxy)- N- hydroxyheptanamide hydrochlorideIC500.31 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(4- (((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5-(3- hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)methyl)-3- methylphenyl)-N- hydroxyacrylamide formateIC500.31 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(4-(((1-(3- Cyano-4-(4-cyano-3- fluorophenyl)-5-(3- hydroxy-4-methoxy- phenyl)pyridin- 2-yl)piperidin-4- yl)(methyl)amino) methyl)phenyl)-N- hydroxyacrylamide formateIC500.33 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
2-(4-(2-((1-(3- Cyano-4-(4- cyano-3- fluorophenyl)-5- (3-hydroxy-4- methoxyphenyl) pyridin-2- yl)piperidin-4- yl)amino)ethyl) phenyl)-N- hydroxyacetamide formateIC500.33 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
US10723742, Example 128IC500.34 nMUS-12435128: Method for predicting therapeutic effect of LSD1 inhibitor based on expression of INSM1
7-(4-(5-(3-amino-8-azabicyclo[3.2.1]octane-8-carbonyl)-3-(4-cyano-3-fluorophenyl)thiophen-2-yl)-2-hydroxyphenoxy)-N-hydroxyheptanamide hydrochlorideIC500.35 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
4-(4-((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5- (3-hydroxy-4- methoxyphenyl) pyridin-2- yl)piperidin-4- yl)amino)methyl) piperidin-1-yl)-N- hydroxybenzamide formateIC500.35 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(5- (((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5-(1-(2- hydroxy-2- methylpropyl)-1H- benzo[d][1,2,3]triazol- 5-yl)pyridin-2- yl)piperidin-4- yl)amino)methyl) pyridin- 2-)-N- hydroxyacrylamide formateIC500.35 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
4-[5-[1-[(1S,2S,4R)-2-amino-7-azabicyclo[2.2.1]heptan-7-yl]ethyl]-2-(2-fluoro-4-methylphenyl)phenyl]-2-fluorobenzonitrileIC500.36 nMUS-11510915: Anti-tumor effect potentiator using novel biphenyl compound
(E)-3-(4-(2-((1-(3- Cyano-4-(4-cyano-3- fluorophenyl)-5-(3- hydroxy-4- methoxyphenyl) pyridin- 2-yl)piperidin-4- yl)amino)ethyl) phenyl)-N- hydroxyacrylamide hydrochlorideIC500.36 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
(E)-3-(5-((1-(3- Cyano-4-(4- cyano-3- fluorophenyl)-5- (3-hydroxy-4- methoxyphenyl) pyridin-2- yl)piperidin-4- yl)amino)methyl) pyridin-2-yl)-N- hydroxyacrylamide formateIC500.36 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
2-(4-((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5- (3-hydroxy-4- methoxyphenyl) pyridin-2- yl)piperidin-4- yl)amino)methyl) phenyl)-N- hydroxycyclopropane- 1- carboxamide formateIC500.37 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF
2-(4-((1-(3-Cyano- 4-(4-cyano-3- fluorophenyl)-5- (3-hydroxy-4- methoxyphenyl) pyridin-2- yl)piperidin-4- yl)amino)methyl)- 2- methoxyphenoxy)- N- hydroxyacetamide formateIC500.39 nMUS-20250304549: HYDROXYAMIDE DERIVATIVE AND USE THEREOF

ChEMBL bioactivities

5725 potent at pChembl≥5 of 6100 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
10.30IC500.05nMCHEMBL4798849
10.22IC500.06nMCHEMBL4762799
10.22IC500.06nMCHEMBL5970037
10.21IC500.062nMCHEMBL6002210
10.15IC500.07nMCHEMBL5767321
10.12IC500.075nMCHEMBL6032207
10.12IC500.076nMCHEMBL6012501
10.05IC500.09nMCHEMBL5855787
10.04IC500.091nMCHEMBL5822088
10.03IC500.093nMCHEMBL5942048
10.00IC500.1nMCHEMBL4639944
10.00IC500.1nMCHEMBL4785635
10.00EC500.1nMCHEMBL4206770
10.00IC500.1nMCHEMBL5878568
10.00IC500.1nMCHEMBL5756723
10.00IC500.1nMCHEMBL5916616
9.96IC500.11nMCHEMBL5864257
9.96IC500.11nMCHEMBL5816140
9.92IC500.12nMCHEMBL5916881
9.92IC500.12nMCHEMBL5748636
9.92IC500.12nMCHEMBL5768539
9.89IC500.13nMCHEMBL4632810
9.89IC500.13nMCHEMBL4639941
9.89IC500.13nMCHEMBL6058075
9.89IC500.13nMCHEMBL5942958
9.85IC500.14nMCHEMBL4641768
9.85IC500.14nMCHEMBL3906257
9.85IC500.14nMVAFIDEMSTAT
9.85IC500.14nMCHEMBL5968979
9.85IC500.14nMCHEMBL6019662
9.85IC500.14nMCHEMBL6056959
9.85IC500.14nMCHEMBL5978892
9.85IC500.14nMCHEMBL5815919
9.85IC500.14nMCHEMBL5872743
9.85IC500.14nMCHEMBL5816040
9.82IC500.15nMCHEMBL4776338
9.82IC500.15nMCHEMBL4776575
9.82IC500.15nMCHEMBL5970037
9.82IC500.15nMCHEMBL5956161
9.82IC500.15nMCHEMBL5956539
9.82IC500.15nMCHEMBL5775148
9.82IC500.15nMCHEMBL5759794
9.80IC500.16nMCHEMBL4642214
9.80IC500.16nMCHEMBL5956539
9.80IC500.16nMCHEMBL5775148
9.77IC500.17nMCHEMBL4635889
9.77IC500.17nMCHEMBL5859070
9.74IC500.18nMCHEMBL4649085
9.74IC500.18nMCHEMBL4759347
9.74IC500.18nMCHEMBL5916881

PubChem BioAssay actives

2020 with measured affinity, of 4823 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.

CompoundAssayTypeValueUnit
5-[1-[3-[4-(azepan-4-yloxy)phenyl]propyl]-4-propylimidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0001uM
5-[4-cyclobutyl-1-[3-(4-piperidin-4-yloxyphenyl)propyl]imidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0001uM
5-[1-[2-[4-(azepan-4-yloxy)phenoxy]ethyl]-4-propylimidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0001uM
4-methyl-5-[1-[3-[4-(piperidin-4-ylmethoxy)phenyl]propyl]-4-propylimidazol-2-yl]thieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0001uM
1-methyl-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0001uM
1-(2-chloroethyl)-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0001uM
1-ethyl-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0001uM
1-(2-fluoroethyl)-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0001uM
N-[3-(ethoxymethyl)-2-[[4-[[(3S)-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methylthieno[3,2-b]pyrrole-5-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0001uM
5-[[[(1R,2S)-2-(4-phenylmethoxyphenyl)cyclopropyl]amino]methyl]-1,3,4-oxadiazol-2-amine1872409: Inhibition of KDM1A (unknown origin)ic500.0001uM
4-N-[(1R,2S)-2-phenylcyclopropyl]cyclohexane-1,4-diamine1759290: Inhibition of LSD1 (unknown origin)ic500.0001uM
5-[1-[2-[4-(azepan-4-yloxy)phenoxy]ethyl]-4-cyclobutylimidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0002uM
5-[1-[3-[4-(azepan-4-yloxy)phenyl]propyl]-4-cyclobutylimidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0002uM
5-[1-[3-[4-(azepan-4-yloxy)phenyl]propyl]-4-ethylimidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0002uM
5-[4-cyclobutyl-1-[2-(4-piperidin-4-yloxyphenoxy)ethyl]imidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0002uM
4-methyl-5-[1-[3-(4-piperidin-4-yloxyphenyl)propyl]-4-propylimidazol-2-yl]thieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0002uM
4-methyl-5-[1-[2-(4-piperidin-4-yloxyphenoxy)ethyl]-4-propylimidazol-2-yl]thieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0002uM
N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]-1-propan-2-ylindole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0002uM
4-N-[(1R,2S)-2-phenylcyclopropyl]cyclohexane-1,4-diamine;dihydrochloride2086562: Inhibition of recombinant human LSD1 assessed as fluorescent intensity using Bio-H3Kme1 as substrate measured after 1 hr by HTRF assayic500.0002uM
4-[2-(4-aminopiperidin-1-yl)-5-(3-fluoro-4-methoxyphenyl)-1-methyl-6-oxopyrimidin-4-yl]-2-fluorobenzonitrile1964559: Inhibition of LSD1 (unknown origin)ic500.0003uM
4-[2-(4-aminopiperidin-1-yl)-5-(3-fluoro-4-methoxyphenyl)-1-methyl-6-oxopyrimidin-4-yl]-2-fluorobenzonitrile;benzenesulfonic acid1698714: Inhibition of LSD1 (unknown origin) using H3K4me1 substrate by TR-FRET assayic500.0003uM
5-[4-cyclobutyl-1-[3-[4-(piperidin-4-ylmethoxy)phenyl]propyl]imidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0003uM
5-[4-ethyl-1-[3-[4-(pyrrolidin-3-ylmethoxy)phenyl]propyl]imidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0003uM
5-[4-ethyl-1-[3-[4-(piperidin-4-ylmethoxy)phenyl]propyl]imidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0003uM
5-[1-[2-[4-(azepan-4-yloxy)phenoxy]ethyl]-4-ethylimidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0003uM
4-methyl-5-[4-propyl-1-[3-[4-(pyrrolidin-3-ylmethoxy)phenyl]propyl]imidazol-2-yl]thieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0003uM
5-[4-ethyl-1-[3-(4-piperidin-4-yloxyphenyl)propyl]imidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0003uM
5-[4-cyclobutyl-1-[3-[4-(pyrrolidin-3-ylmethoxy)phenyl]propyl]imidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0004uM
1-(difluoromethyl)-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0004uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149874: Binding affinity to human KDM1A incubated for 45 mins by Kinobead based pull down assaykd0.0004uM
4-[6-(4-aminopiperidin-1-yl)-4-methyl-3-(4-methylphenyl)-5-oxopyrazin-2-yl]-2-fluorobenzonitrile1698714: Inhibition of LSD1 (unknown origin) using H3K4me1 substrate by TR-FRET assayic500.0005uM
N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]-1H-indole-4-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0005uM
N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]-1-benzofuran-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0005uM
5-fluoro-1-methyl-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0005uM
5-[4-ethyl-1-[2-(4-piperidin-4-yloxyphenoxy)ethyl]imidazol-2-yl]-4-methylthieno[3,2-b]pyrrole1655404: Inhibition of recombinant human LSD1 expressed in Escherichia coli using biotinylated H3K4me as substrate by TR-FRET assayic500.0006uM
4-[2-(4-aminopiperidin-1-yl)-5-(4-methoxyphenyl)-1-methyl-6-oxopyrimidin-4-yl]benzonitrile1698714: Inhibition of LSD1 (unknown origin) using H3K4me1 substrate by TR-FRET assayic500.0007uM
4-[1-(3-chloro-2-methylindazol-5-yl)-5-methyl-4-[(3S)-3-(methylamino)pyrrolidine-1-carbonyl]imidazol-2-yl]-2-fluorobenzonitrile1514202: Inhibition of LSD1 (unknown origin)ic500.0007uM
4-[2-(4-aminopiperidin-1-yl)-5-(3-fluoro-4-methoxyphenyl)-1-methyl-6-oxopyrimidin-4-yl]benzonitrile1698714: Inhibition of LSD1 (unknown origin) using H3K4me1 substrate by TR-FRET assayic500.0008uM
1-(2,2-difluoroethyl)-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0008uM
trans-(1R,2S)-2-(3,4-difluorophenyl)-N-[[1-(4-piperidin-1-ylphenyl)triazol-4-yl]methyl]cyclopropan-1-amine;hydrochloride2086562: Inhibition of recombinant human LSD1 assessed as fluorescent intensity using Bio-H3Kme1 as substrate measured after 1 hr by HTRF assayic500.0008uM
N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]-1,3-benzothiazole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0009uM
N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]-1-benzothiophene-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0009uM
4-[(1S,2R)-2-(cyclopropylmethylamino)cyclopropyl]-N-phenylbenzamide1986223: Inhibition of LSD1 (unknown origin)ic500.0010uM
4-[1-(3-chloro-2-methylindazol-5-yl)-5-methyl-4-[(3R)-3-(methylamino)piperidine-1-carbonyl]imidazol-2-yl]-2-fluorobenzonitrile1514202: Inhibition of LSD1 (unknown origin)ic500.0010uM
1-methyl-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indazole-3-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0010uM
6-chloro-1-methyl-N-[1-[(4-piperidin-4-yloxyphenyl)methyl]-3,4-dihydro-2H-quinolin-8-yl]indole-2-carboxamide1691613: Inhibition of human recombinant LSD1 using fluorogenic ADHP based substrate preincubated for 30 mins followed by substrate addition measured after 10 mins by horseradish peroxidase coupled fluorescence assayic500.0011uM
N-[(2-fluorophenyl)methyl]spiro[1,2-dihydroindene-3,2’-cyclopropane]-1’-amine1755617: Inhibition of human LSD1 (172 to 852 residues) using Bio-H3K4me2 (1 to 24 residues) as substrate incubated for 1 hr by TR-FRET assayic500.0011uM
trans-(1R,2S)-2-(3,4-difluorophenyl)-N-[[1-(4-pyrrolidin-1-ylphenyl)triazol-4-yl]methyl]cyclopropan-1-amine;hydrochloride2086562: Inhibition of recombinant human LSD1 assessed as fluorescent intensity using Bio-H3Kme1 as substrate measured after 1 hr by HTRF assayic500.0012uM
4-[5-(4-methyl-2,3-dihydro-1,4-benzoxazin-7-yl)-1-[(4-methylpiperidin-4-yl)methyl]pyrrolo[2,3-c]pyridin-4-yl]benzonitrile2016730: Inhibition of human recombinant LSD1 expressed in Escherichia coli using H3K4me2 peptide as substrate incubated for 60 mins by AlphaLISA assayic500.0013uM
4-[6-(4-aminopiperidin-1-yl)-4-methyl-3-(4-methylphenyl)-5-oxopyrazin-2-yl]benzonitrile1698714: Inhibition of LSD1 (unknown origin) using H3K4me1 substrate by TR-FRET assayic500.0014uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, affects cotreatment, increases methylation, decreases expression, increases abundance4
Benzo(a)pyreneaffects cotreatment, affects localization, affects binding, increases reaction, increases methylation3
Tretinoindecreases expression, affects localization3
sodium arsenitedecreases expression2
Polyaminesdecreases activity2
Valproic Aciddecreases expression, affects cotreatment, increases expression2
SP2509decreases stability, affects binding, decreases expression, decreases reaction1
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases expression1
TAK-243increases sumoylation1
ginger extractaffects cotreatment, affects expression, increases abundance1
2,4,6-tribromophenoldecreases expression1
triphenyl phosphateaffects expression1
4-biphenylamineaffects cotreatment, affects localization1
decabromobiphenyl etherdecreases expression1
cobaltous chloridedecreases expression1
tetrabromobisphenol Adecreases expression1
perfluorooctanoic aciddecreases expression1
coumarinincreases phosphorylation1
testosterone-3-carboxymethyloxime-bovine serum albumin conjugateaffects expression1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridineaffects cotreatment, affects localization, increases expression1
benzyloxycarbonylleucyl-leucyl-leucine aldehydedecreases reaction, decreases stability1
perfluorooctane sulfonic aciddecreases expression1
K 7174decreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
enzalutamideincreases reaction, decreases expression1
NSC 689534affects binding, decreases expression1
MK-8776decreases expression1

ChEMBL screening assays

1089 unique, capped per target: 1075 binding, 7 functional, 7 admet

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3110656BindingInhibition of recombinant human LSD1/CoREST complex expressed in Escherichia coli using methylated H3-K4 peptide as substrate by peroxidase-coupled assaySynthesis and evaluation of novel cyclic Peptide inhibitors of lysine-specific demethylase 1. — ACS Med Chem Lett
CHEMBL3215162FunctionalPubChem BioAssay. qHTS Assay for Inhibitors of Human Jumonji Domain Containing 2E (JMJD2E): Counterscreen with LSD1. (Class of assay: confirmatory)PubChem BioAssay data set
CHEMBL3777866ADMETDrug metabolism assessed as LSD1 (unknown origin)-mediated demethylation of compound by measuring (3S,6S,9S,12S)-1-((S)-1-((S)-6-amino-2-((S)-2-((S)-4-amino-2-((S)-1-((S)-3-carboxy-2-((S)-2-((S)-1-((6S,9S,12S,15S,18S,21S,24S)-1,28-diamino-2Identification of SNAIL1 Peptide-Based Irreversible Lysine-Specific Demethylase 1-Selective Inactivators. — J Med Chem

Cellosaurus cell lines

12 cell lines: 9 cancer cell line, 3 embryonic stem cell

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

CellosaurusNameCategorySex
CVCL_A3L3SEES3-1V human KDM1A, clone1Embryonic stem cellMale
CVCL_A3L4SEES3-1V human KDM1A, clone2Embryonic stem cellMale
CVCL_A3L5SEES3-1V human KDM1A, clone3Embryonic stem cellMale
CVCL_B1V3Abcam HeLa KDM1A KOCancer cell lineFemale
CVCL_B8J3Abcam HCT 116 KDM1A KOCancer cell lineMale
CVCL_B8XXAbcam MCF-7 KDM1A KOCancer cell lineFemale
CVCL_B9LEAbcam A-549 KDM1A KOCancer cell lineMale
CVCL_D7T5Ubigene A-549 KDM1A KOCancer cell lineMale
CVCL_D8NUUbigene HCT 116 KDM1A KOCancer cell lineMale
CVCL_E0G1Ubigene HeLa KDM1A KOCancer cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT00368004Not specifiedTERMINATEDFamily Studies of Uveal Coloboma
NCT01778543Not specifiedRECRUITINGPathogenesis and Genetics of Microphthalmia, Anophthalmia and Uveal Coloboma (MAC)
NCT04833361Not specifiedCOMPLETEDPotential Environmental Causes of Uveal Coloboma
NCT06293560Not specifiedRECRUITINGMicrophthalmia, Anophthalmia, and Coloboma Genetic Epidemiology in Children
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

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This page pulls from 81 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgtopdb_interactiongwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpatentpatent_compoundpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot