Details of the Target

General Information of Target

Target ID LDTP13233
Target Name Lysine-specific demethylase 5B (KDM5B)
Gene Name KDM5B
Gene ID 10765
Synonyms
JARID1B; PLU1; RBBP2H1; Lysine-specific demethylase 5B; EC 1.14.11.67; Cancer/testis antigen 31; CT31; Histone demethylase JARID1B; Jumonji/ARID domain-containing protein 1B; PLU-1; Retinoblastoma-binding protein 2 homolog 1; RBP2-H1; [histone H3]-trimethyl-L-lysine(4) demethylase 5B
3D Structure
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2D Sequence (FASTA)
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3D Structure (PDB)
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Sequence
MEREPSASEAAPAAAALFAWGANSYGQLGLGHKEDVLLPQQLNDFCKPRSVRRITGGGGH
SAVVTDGGDLFVCGLNKDGQLGLGHTEDIPYFTPCKSLFGCPIQQVACGWDFTIMLTENG
QVLSCGSNSFGQLGVPHGPRRCVVPQAIELHKEKVVCIAAGLRHAVAATASGIVFQWGTG
LASCGRRLCPGQTLPLFFTAKEPSRVTGLENSKAMCVLAGSDHSASLTDAGEVYVWGSNK
HGQLANEAAFLPVPQKIEAHCFQNEKVTAIWSGWTHLVAQTETGKMFTWGRADYGQLGRK
LETYEGWKLEKQDSFLPCSRPPNSMPSSPHCLTGATEVSCGSEHNLAIIGGVCYSWGWNE
HGMCGDGTEANVWAPKPVQALLSSSGLLVGCGAGHSLALCQLPAHPALVQDPKVTYLSPD
AIEDTESQKAMDKERNWKERQSETSTQSQSDWSRNGGL
Target Type
Literature-reported
Target Bioclass
Enzyme
Family
JARID1 histone demethylase family
Subcellular location
Nucleus
Function
Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma. Represses the CLOCK-BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2.
TTD ID
T56871
Uniprot ID
Q9UGL1
DrugMap ID
TTCLI75
Ensemble ID
ENST00000367264.7
HGNC ID
HGNC:18039
ChEMBL ID
CHEMBL3774295

Target Site Mutations in Different Cell Lines

Cell line Mutation details Probe for labeling this protein in this cell
A3KAW SNV: p.R98H .
CAL51 SNV: p.D606V DBIA    Probe Info 
CCK81 Deletion: p.L1339SfsTer8 .
HCC827 SNV: p.F1077L .
HCT15 SNV: p.R1253Ter .
HEC1 SNV: p.E57Ter; p.S222L; p.R1241H .
HEC1B SNV: p.E57Ter; p.S222L .
HEPG2 SNV: p.Y1457H .
ICC3 Insertion: p.S38RfsTer26 DBIA    Probe Info 
J82 SNV: p.R1416T DBIA    Probe Info 
LS180 Deletion: p.S1119AfsTer4
SNV: p.A1540T		 .
LU65 SNV: p.P68L .
MCC26 Substitution: p.D1445N DBIA    Probe Info 
NB1 SNV: p.C338R DBIA    Probe Info 
NCIH1048 SNV: p.W513Ter DBIA    Probe Info 
NCIH1666 SNV: p.E418Q DBIA    Probe Info 
SKMEL30 SNV: p.T1044K DBIA    Probe Info 
SNU1 SNV: p.D1197E DBIA    Probe Info 
TF1 SNV: p.K535Ter .
YSCCC SNV: p.D387H DBIA    Probe Info 

Probe(s) Labeling This Target

ABPP Probe
Click To Hide/Show 8 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
DBIA
 Probe Info  		C650(2.13)  LDD3310  [1]
AHL-Pu-1
 Probe Info  		C1072(2.91)  LDD0168  [2]
W1
 Probe Info  		D806(0.51); E808(0.51); K809(0.51)  LDD0238  [3]
IA-alkyne
 Probe Info  		C574(0.00); C1094(0.00)  LDD0165  [4]
NAIA_5
 Probe Info  		C193(0.00); C62(0.00)  LDD2225  [5]
IPM
 Probe Info  		C193(0.00); C62(0.00); C1094(0.00)  LDD2156  [6]
TFBX
 Probe Info  		C810(0.00); C1094(0.00); C574(0.00)  LDD0148  [7]
YN-1
 Probe Info  		N.A.  LDD0447  [8]

Competitor(s) Related to This Target

Competitor ID Name Cell line Binding Site(Ratio) Interaction ID Ref
 LDCM0025  4SU-RNA HEK-293T C1072(2.91)  LDD0168  [2]
 LDCM0026  4SU-RNA+native RNA HEK-293T C1072(5.69)  LDD0169  [2]
 LDCM0237  AC12 HEK-293T C147(0.92)  LDD1510  [9]
 LDCM0280  AC20 HEK-293T C147(0.97)  LDD1519  [9]
 LDCM0284  AC24 HEK-293T C147(0.99); C854(1.03)  LDD1523  [9]
 LDCM0288  AC28 HEK-293T C147(0.93)  LDD1527  [9]
 LDCM0293  AC32 HEK-293T C147(1.12); C854(1.05)  LDD1532  [9]
 LDCM0297  AC36 HEK-293T C147(1.03)  LDD1536  [9]
 LDCM0301  AC4 HEK-293T C147(1.11)  LDD1540  [9]
 LDCM0302  AC40 HEK-293T C147(1.15); C854(1.05)  LDD1541  [9]
 LDCM0306  AC44 HEK-293T C147(1.14)  LDD1545  [9]
 LDCM0310  AC48 HEK-293T C147(0.99); C854(1.26)  LDD1549  [9]
 LDCM0315  AC52 HEK-293T C147(0.96)  LDD1554  [9]
 LDCM0319  AC56 HEK-293T C147(1.01); C854(0.98)  LDD1558  [9]
 LDCM0324  AC60 HEK-293T C147(1.10)  LDD1563  [9]
 LDCM0328  AC64 HEK-293T C147(0.91); C854(1.17)  LDD1567  [9]
 LDCM0345  AC8 HEK-293T C147(1.30); C854(1.03)  LDD1569  [9]
 LDCM0275  AKOS034007705 HEK-293T C147(1.11); C854(0.93)  LDD1514  [9]
 LDCM0369  CL100 HEK-293T C147(1.11)  LDD1573  [9]
 LDCM0372  CL103 HEK-293T C147(1.08)  LDD1576  [9]
 LDCM0373  CL104 HEK-293T C147(0.84)  LDD1577  [9]
 LDCM0376  CL107 HEK-293T C147(1.13)  LDD1580  [9]
 LDCM0377  CL108 HEK-293T C147(0.80)  LDD1581  [9]
 LDCM0381  CL111 HEK-293T C147(1.10)  LDD1585  [9]
 LDCM0382  CL112 HEK-293T C147(0.97)  LDD1586  [9]
 LDCM0385  CL115 HEK-293T C147(1.26)  LDD1589  [9]
 LDCM0386  CL116 HEK-293T C147(0.87)  LDD1590  [9]
 LDCM0389  CL119 HEK-293T C147(1.35)  LDD1593  [9]
 LDCM0390  CL12 HEK-293T C147(1.46); C854(1.17)  LDD1594  [9]
 LDCM0391  CL120 HEK-293T C147(0.95)  LDD1595  [9]
 LDCM0394  CL123 HEK-293T C147(1.08)  LDD1598  [9]
 LDCM0395  CL124 HEK-293T C147(0.73)  LDD1599  [9]
 LDCM0398  CL127 HEK-293T C147(1.18)  LDD1602  [9]
 LDCM0399  CL128 HEK-293T C147(0.74)  LDD1603  [9]
 LDCM0402  CL15 HEK-293T C147(1.03)  LDD1606  [9]
 LDCM0403  CL16 HEK-293T C147(1.03)  LDD1607  [9]
 LDCM0408  CL20 HEK-293T C147(0.93)  LDD1612  [9]
 LDCM0412  CL24 HEK-293T C147(1.69); C854(0.98)  LDD1616  [9]
 LDCM0415  CL27 HEK-293T C147(1.02)  LDD1619  [9]
 LDCM0416  CL28 HEK-293T C147(0.91)  LDD1620  [9]
 LDCM0418  CL3 HEK-293T C147(1.29)  LDD1622  [9]
 LDCM0421  CL32 HEK-293T C147(0.92)  LDD1625  [9]
 LDCM0425  CL36 HEK-293T C147(1.83); C854(0.98)  LDD1629  [9]
 LDCM0428  CL39 HEK-293T C147(1.19)  LDD1632  [9]
 LDCM0429  CL4 HEK-293T C147(1.05)  LDD1633  [9]
 LDCM0430  CL40 HEK-293T C147(0.97)  LDD1634  [9]
 LDCM0434  CL44 HEK-293T C147(0.96)  LDD1638  [9]
 LDCM0438  CL48 HEK-293T C147(1.59); C854(0.94)  LDD1642  [9]
 LDCM0443  CL52 HEK-293T C147(1.19)  LDD1646  [9]
 LDCM0447  CL56 HEK-293T C147(1.13)  LDD1650  [9]
 LDCM0452  CL60 HEK-293T C147(1.33); C854(1.04)  LDD1655  [9]
 LDCM0455  CL63 HEK-293T C147(1.37)  LDD1658  [9]
 LDCM0456  CL64 HEK-293T C147(1.14)  LDD1659  [9]
 LDCM0460  CL68 HEK-293T C147(0.97)  LDD1663  [9]
 LDCM0465  CL72 HEK-293T C147(1.52); C854(0.88)  LDD1668  [9]
 LDCM0469  CL76 HEK-293T C147(0.83)  LDD1672  [9]
 LDCM0473  CL8 HEK-293T C147(1.19)  LDD1676  [9]
 LDCM0474  CL80 HEK-293T C147(1.02)  LDD1677  [9]
 LDCM0478  CL84 HEK-293T C147(1.13); C854(1.00)  LDD1681  [9]
 LDCM0481  CL87 HEK-293T C147(1.22)  LDD1684  [9]
 LDCM0482  CL88 HEK-293T C147(0.64)  LDD1685  [9]
 LDCM0487  CL92 HEK-293T C147(0.95)  LDD1690  [9]
 LDCM0491  CL96 HEK-293T C147(0.97); C854(1.06)  LDD1694  [9]
 LDCM0494  CL99 HEK-293T C147(1.39)  LDD1697  [9]
 LDCM0495  E2913 HEK-293T C147(1.09)  LDD1698  [9]
 LDCM0468  Fragment33 HEK-293T C147(1.08)  LDD1671  [9]
 LDCM0022  KB02 HEK-293T C147(0.97)  LDD1492  [9]
 LDCM0023  KB03 HEK-293T C147(0.82)  LDD1497  [9]
 LDCM0024  KB05 COLO792 C650(2.13)  LDD3310  [1]
 LDCM0111  W14 Hep-G2 D806(0.51); E808(0.51); K809(0.51)  LDD0238  [3]

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
Transcriptional repressor CTCF (CTCF) CTCF zinc-finger protein family P49711

The Drug(s) Related To This Target

Investigative
Click To Hide/Show 1 Drug(s) Interacting with This Target
Drug Name Drug Type External ID
Pbit Small molecular drug D0IQ7Y

References

1 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
2 Chemoproteomic capture of RNA binding activity in living cells. Nat Commun. 2023 Oct 7;14(1):6282. doi: 10.1038/s41467-023-41844-z.
Mass spectrometry data entry: PXD044625
3 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.
4 SP3-FAIMS Chemoproteomics for High-Coverage Profiling of the Human Cysteinome*. Chembiochem. 2021 May 14;22(10):1841-1851. doi: 10.1002/cbic.202000870. Epub 2021 Feb 18.
Mass spectrometry data entry: PXD023056 , PXD023059 , PXD023058 , PXD023057 , PXD023060
5 N-Acryloylindole-alkyne (NAIA) enables imaging and profiling new ligandable cysteines and oxidized thiols by chemoproteomics. Nat Commun. 2023 Jun 15;14(1):3564. doi: 10.1038/s41467-023-39268-w.
Mass spectrometry data entry: PXD041264
6 Benchmarking Cleavable Biotin Tags for Peptide-Centric Chemoproteomics. J Proteome Res. 2022 May 6;21(5):1349-1358. doi: 10.1021/acs.jproteome.2c00174. Epub 2022 Apr 25.
Mass spectrometry data entry: PXD031019
7 Chemoproteomic Profiling by Cysteine Fluoroalkylation Reveals Myrocin G as an Inhibitor of the Nonhomologous End Joining DNA Repair Pathway. J Am Chem Soc. 2021 Dec 8;143(48):20332-20342. doi: 10.1021/jacs.1c09724. Epub 2021 Nov 24.
Mass spectrometry data entry: PXD029255
8 Ynamide Electrophile for the Profiling of Ligandable Carboxyl Residues in Live Cells and the Development of New Covalent Inhibitors. J Med Chem. 2022 Aug 11;65(15):10408-10418. doi: 10.1021/acs.jmedchem.2c00272. Epub 2022 Jul 26.
9 Accelerating multiplexed profiling of protein-ligand interactions: High-throughput plate-based reactive cysteine profiling with minimal input. Cell Chem Biol. 2024 Mar 21;31(3):565-576.e4. doi: 10.1016/j.chembiol.2023.11.015. Epub 2023 Dec 19.
Mass spectrometry data entry: PXD044402