Details of the Target

General Information of Target

Target ID LDTP11440
Target Name Lysine-specific demethylase 5D (KDM5D)
Gene Name KDM5D
Gene ID 8284
Synonyms
HY; HYA; JARID1D; KIAA0234; SMCY; Lysine-specific demethylase 5D; EC 1.14.11.67; Histocompatibility Y antigen; H-Y; Histone demethylase JARID1D; Jumonji/ARID domain-containing protein 1D; Protein SmcY; [histone H3]-trimethyl-L-lysine(4) demethylase 5D
3D Structure
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2D Sequence (FASTA)
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3D Structure (PDB)
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Sequence
MALKWTSVLLLIHLGCYFSSGSCGKVLVWTGEYSHWMNMKTILKELVQRGHEVTVLASSA
SILFDPNDAFTLKLEVYPTSLTKTEFENIIMQQVKRWSDIQKDSFWLYFSQEQEILWEFH
DIFRNFCKDVVSNKKVMKKLQESRFDIIFADAFFPCGELLAALLNIPFVYSLCFTPGYTI
ERHSGGLIFPPSYIPVVMSKLSDQMTFMERVKNMIYVLYFDFWFQMCDMKKWDQFYSEVL
GRPTTLFETMGKADIWLMRNSWSFQFPHPFLPNIDFVGGLHCKPAKPLPKEMEEFVQSSG
ENGVVVFSLGSVISNMTAERANVIATALAKIPQKVLWRFDGNKPDALGLNTRLYKWIPQN
DLLGLPKTRAFITHGGANGIYEAIYHGIPMVGIPLFWDQPDNIAHMKAKGAAVRLDFHTM
SSTDLLNALKTVINDPSYKENVMKLSIIQHDQPVKPLHRAVFWIEFVMCHKGAKHLRVAA
RDLTWFQYHSLDVIGFLLACVATVIFVVTKFCLFCFWKFARKGKKGKRD
Target Bioclass
Enzyme
Family
JARID1 histone demethylase family
Subcellular location
Nucleus
Function
Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May play a role in spermatogenesis. Involved in transcriptional repression of diverse metastasis-associated genes; in this function seems to cooperate with ZMYND8. Suppresses prostate cancer cell invasion. Regulates androgen receptor (AR) transcriptional activity by demethylating H3K4me3 active transcription marks.
Uniprot ID
Q9BY66
Ensemble ID
ENST00000317961.9
HGNC ID
HGNC:11115
ChEMBL ID
CHEMBL5169191

Target Site Mutations in Different Cell Lines

Cell line Mutation details Probe for labeling this protein in this cell
LN18 SNV: p.S759C .
MEWO SNV: p.P1523L .
NCIH1703 SNV: p.A974S .
OCILY3 SNV: p.A1284S .
U118MG SNV: p.T1084R .

Probe(s) Labeling This Target

ABPP Probe
Click To Hide/Show 5 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
IPM
 Probe Info  		N.A.  LDD0241  [1]
Alkylaryl probe 2
 Probe Info  		3.00  LDD0390  [2]
DBIA
 Probe Info  		C265(1.54)  LDD2348  [3]
YY4-yne
 Probe Info  		2.94  LDD0400  [4]
Acrolein
 Probe Info  		N.A.  LDD0217  [5]

Competitor(s) Related to This Target

Competitor ID Name Cell line Binding Site(Ratio) Interaction ID Ref
 LDCM0022  KB02 HD-MY-Z C265(1.54)  LDD2348  [3]
 LDCM0023  KB03 HD-MY-Z C265(2.11)  LDD2765  [3]
 LDCM0024  KB05 HD-MY-Z C265(2.28)  LDD3182  [3]
 LDCM0099  Phenelzine HEK-293T 3.00  LDD0390  [2]
 LDCM0154  YY4 T cell 2.94  LDD0400  [4]

The Interaction Atlas With This Target

The Protein(s) Related To This Target

Transcription factor
Click To Hide/Show 1 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Androgen receptor (AR) Nuclear hormone receptor family P10275

The Drug(s) Related To This Target

Approved
Click To Hide/Show 1 Drug(s) Interacting with This Target
Drug Name Drug Type External ID
Ascorbic Acid Small molecular drug DB00126

References

1 Oxidant-Induced Bioconjugation for Protein Labeling in Live Cells. ACS Chem Biol. 2023 Jan 20;18(1):112-122. doi: 10.1021/acschembio.2c00740. Epub 2022 Dec 21.
2 Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes. bioRxiv, 2020-06.
3 DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. Cell. 2024 May 9;187(10):2536-2556.e30. doi: 10.1016/j.cell.2024.03.027. Epub 2024 Apr 22.
Mass spectrometry data entry: PXD047840
4 A Chemical Proteomic Probe for the Mitochondrial Pyruvate Carrier Complex. Angew Chem Int Ed Engl. 2020 Mar 2;59(10):3896-3899. doi: 10.1002/anie.201914391. Epub 2020 Feb 11.
5 ACR-Based Probe for the Quantitative Profiling of Histidine Reactivity in the Human Proteome. J Am Chem Soc. 2023 Mar 8;145(9):5252-5260. doi: 10.1021/jacs.2c12653. Epub 2023 Feb 27.