mutated Ligand Binding Site gene DataBase





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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for KDM5B
Gene summary
Basic gene Info.Gene symbolKDM5B
Gene namelysine (K)-specific demethylase 5B
CytomapUCSC genome browser: 1q32.1
Type of geneprotein-coding
DescriptionRBP2-H1cancer/testis antigen 31histone demethylase JARID1Bjumonji, AT rich interactive domain 1Bjumonji/ARID domain-containing protein 1Blysine-specific demethylase 5Bprotein phosphatase 1, regulatory subunit 98putative DNA/chromatin binding motif
Modification date20141207
dbXrefs MIM : 605393
Ensembl : ENSG00000117139
HPRD : 09251
Vega : OTTHUMG00000041401
ProteinUniProt: Q9UGL1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM5B
BioGPS: 10765
PathwayNCI Pathway Interaction Database: KDM5B
Pathway Commons: KDM5B
ContextiHOP: KDM5B
ligand binding site mutation search in PubMed: KDM5B
UCL Cancer Institute: KDM5B
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0034720histone H3-K4 demethylation20228790
GO:0034721histone H3-K4 demethylation, trimethyl-H3-K4-specific20228790
GO:0045892negative regulation of transcription, DNA-templated12657635

Ligand binding site mutations for KDM5B
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

Protein structure related information for KDM5B
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for KDM5B from PDB

Differential gene expression and gene-gene network for KDM5B
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of KDM5B and the right PPI network was created from samples without mutations in the LBS of KDM5B. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for KDM5B
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for KDM5B
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of KDM5B go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of KDM5B
Multiple alignments for Q9UGL1 in multiple species
LBSAA sequence# speciesSpecies
A599FNFAEAVNFCT4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
A599LNFAEAVNFAP1Caenorhabditis elegans
C1487DEDAICPAVSC2Homo sapiens, Mus musculus
C1487SEFKSCQARAC1Caenorhabditis elegans
C1487EDMTLCPAESC1Danio rerio
C1487DEDAICPAVTC1Gallus gallus
C1492CPAVSCLQPEG2Homo sapiens, Mus musculus
C1492CQARACLKPYG1Caenorhabditis elegans
C1492CPAESCLQPEG1Danio rerio
C1492CPAVTCLQPEG1Gallus gallus
C1505VDWVQCDGSCN3Homo sapiens, Gallus gallus, Mus musculus
C1505VNWVMCEAGCK1Caenorhabditis elegans
C1505VDWVQCD-CCN1Danio rerio
C1509QCDGSCNQWFH3Homo sapiens, Gallus gallus, Mus musculus
C1509MCEAGCKNWFH1Caenorhabditis elegans
C1509QCD-CCNRWFH1Danio rerio
C1517WFHQVCVGVS-2Homo sapiens, Mus musculus
C1517WFHVICLGFTL1Caenorhabditis elegans
C1517WFHMICVGVS-1Danio rerio
C1517WFHQVCVGIS-1Gallus gallus
C1532KEDYICVRC-T2Homo sapiens, Mus musculus
C1532MHEYRCSSCLD1Caenorhabditis elegans
C1532EEDYMCVSC-S1Danio rerio
C1532KEDYICASC-A1Gallus gallus
C1535YICVRC-TVKD1Homo sapiens
C1535YRCSSCLDHAD1Caenorhabditis elegans
C1535YMCVSC-STSH1Danio rerio
C1535YICASC-AGKG1Gallus gallus
C1535YICVRC-TGKD1Mus musculus
C312VDLYVCLLCGS3Homo sapiens, Gallus gallus, Mus musculus
C312MDQVFCVACNE1Caenorhabditis elegans
C312VDLYVCLVCGK1Danio rerio
C315YVCLLCGSGND3Homo sapiens, Gallus gallus, Mus musculus
C315VFCVACNEGKD1Caenorhabditis elegans
C315YVCLVCGKGND1Danio rerio
C327DRLLLC--DGC4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
C327DLLLLCDIDGC1Caenorhabditis elegans
C330C--DGCDDSYH4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
C330CDIDGCNNGRH1Caenorhabditis elegans
C338SYHTFCLIPPL3Homo sapiens, Danio rerio, Gallus gallus
C338GRHTYCCDPVL1Caenorhabditis elegans
C338SYHTFCLVPPL1Mus musculus
C353KGDWRCPKCLA2Homo sapiens, Mus musculus
C353EGEWRCPKCIE1Caenorhabditis elegans
C353KGDWRCPKCLT1Danio rerio
C353KGDWRCPQCLA1Gallus gallus
C356WRCPKCLAQEC2Homo sapiens, Mus musculus
C356WRCPKCIESED1Caenorhabditis elegans
C356WRCPKCLTQEC1Danio rerio
C356WRCPQCLAQEC1Gallus gallus
C692DDERQCVKCKT1Homo sapiens
C692DEQRSCRFCKT1Caenorhabditis elegans
C692DDERQCVKCRT1Danio rerio
C692DDERQCYKCKT1Gallus gallus
C692DDERQCIKCKT1Mus musculus
C695RQCVKCKTTCF1Homo sapiens
C695RSCRFCKTTLF1Caenorhabditis elegans
C695RQCVKCRTTCY1Danio rerio
C695RQCYKCKTTCF1Gallus gallus
C695RQCIKCKTTCF1Mus musculus
C706MSAISCSCKPG2Homo sapiens, Mus musculus
C706MCALVCN-KHK1Caenorhabditis elegans
C706LSALTCPCRPG1Danio rerio
C706MSAVYCPCKPG1Gallus gallus
C708AISCSCKPGLL2Homo sapiens, Mus musculus
C708ALVCN-KHKKM1Caenorhabditis elegans
C708ALTCPCRPGVQ1Danio rerio
C708AVYCPCKPGLL1Gallus gallus
C715PGLLVCLHHVK2Homo sapiens, Mus musculus
C715HKKMTCVEHHD1Caenorhabditis elegans
C715PGVQVCLYHTH1Danio rerio
C715PGLLVCLYHVE1Gallus gallus
C723HVKELC-SCPP2Homo sapiens, Mus musculus
C723HHDHLCNSCTT1Caenorhabditis elegans
C723HTHDLC-SCPI1Danio rerio
C723HVEDLC-SCPT1Gallus gallus
C725ELC-SCPPYKY2Homo sapiens, Mus musculus
C725HLCNSCTTKDY1Caenorhabditis elegans
C725DLC-SCPISNY1Danio rerio
C725DLC-SCPTYQY1Gallus gallus
D308ATNAVDLYVCL1Homo sapiens
D308DEDPMDQVFCV1Caenorhabditis elegans
D308PVSMVDLYVCL1Danio rerio
D308PTSAVDLYVCL1Gallus gallus
D308TATAVDLYVCL1Mus musculus
D328LLC--DGCDDS4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
D328LLCDIDGCNNG1Caenorhabditis elegans
D331--DGCDDSYHT4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
D331DIDGCNNGRHT1Caenorhabditis elegans
D350DVPKGDWRCPK3Homo sapiens, Danio rerio, Mus musculus
D350EVPEGEWRCPK1Caenorhabditis elegans
D350DVPKGDWRCPQ1Gallus gallus
D428VEYGADIASKE4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
D428VKYGADLITSR1Caenorhabditis elegans
E321GSGNDEDRLLL3Homo sapiens, Gallus gallus, Mus musculus
E321NEGKDEDLLLL1Caenorhabditis elegans
E321GKGNDEDRLLL1Danio rerio
E419VSTIEEDVTVE3Homo sapiens, Gallus gallus, Mus musculus
E419VISHENPVSVK1Caenorhabditis elegans
E419VGTIQEDVTVE1Danio rerio
E501FCWHIEDHWSY4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
E501FCWHTEDHWTY1Caenorhabditis elegans
F496MCFSSFCWHIE4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
F496MCFSTFCWHTE1Caenorhabditis elegans
G316VCLLCGSGNDE3Homo sapiens, Gallus gallus, Mus musculus
G316FCVACNEGKDE1Caenorhabditis elegans
G316VCLVCGKGNDE1Danio rerio
G318LLCGSGNDEDR3Homo sapiens, Gallus gallus, Mus musculus
G318VACNEGKDEDL1Caenorhabditis elegans
G318LVCGKGNDEDR1Danio rerio
G349HDVPKGDWRCP3Homo sapiens, Gallus gallus, Mus musculus
G349DEVPEGEWRCP1Caenorhabditis elegans
G349TDVPKGDWRCP1Danio rerio
H1514CNQWFHQVCVG3Homo sapiens, Gallus gallus, Mus musculus
H1514CKNWFHVICLG1Caenorhabditis elegans
H1514CNRWFHMICVG1Danio rerio
H335CDDSYHTFCLI3Homo sapiens, Danio rerio, Gallus gallus
H335CNNGRHTYCCD1Caenorhabditis elegans
H335CDDSYHTFCLV1Mus musculus
H499SSFCWHIEDHW4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
H499STFCWHTEDHW1Caenorhabditis elegans
H587FPRAYHSGFNQ3Homo sapiens, Gallus gallus, Mus musculus
H587FPRAYHAGFNE1Caenorhabditis elegans
H587FPRSYHSGFNQ1Danio rerio
H622HYRLLHRYCVF2Homo sapiens, Mus musculus
H622SYSNVRRYLVF1Caenorhabditis elegans
H622HYRQLHRYCVF1Danio rerio
H622HYRLLSRYCVF1Gallus gallus
H718LVCLHHVKELC2Homo sapiens, Mus musculus
H718MTCVEHHDHLC1Caenorhabditis elegans
H718QVCLYHTHDLC1Danio rerio
H718LVCLYHVEDLC1Gallus gallus
K348LHDVPKGDWRC3Homo sapiens, Gallus gallus, Mus musculus
K348LDEVPEGEWRC1Caenorhabditis elegans
K348LTDVPKGDWRC1Danio rerio
K517HWGEPKTWYGV2Homo sapiens, Mus musculus
K517HWGEPKTWYGA2Danio rerio, Gallus gallus
K517HFGERKIWYGV1Caenorhabditis elegans
K694ERQCVKCKTTC1Homo sapiens
K694QRSCRFCKTTL1Caenorhabditis elegans
K694ERQCVKCRTTC1Danio rerio
K694ERQCYKCKTTC1Gallus gallus
K694ERQCIKCKTTC1Mus musculus
L324NDEDRLLLC--4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
L324KDEDLLLLCDI1Caenorhabditis elegans
L325DEDRLLLC--D4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
L325DEDLLLLCDID1Caenorhabditis elegans
L326EDRLLLC--DG4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
L326EDLLLLCDIDG1Caenorhabditis elegans
L413KEFWRLVSTIE3Homo sapiens, Gallus gallus, Mus musculus
L413RSFWKNVISHE1Caenorhabditis elegans
L413KEFWRLVGTIQ1Danio rerio
L90PRIQRLNELEA4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
L90PRTQKLNEVEA1Caenorhabditis elegans
N319LCGSGNDEDRL3Homo sapiens, Gallus gallus, Mus musculus
N319ACNEGKDEDLL1Caenorhabditis elegans
N319VCGKGNDEDRL1Danio rerio
N509WSYSINYLHWG4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
N509WTYSVNYNHFG1Caenorhabditis elegans
N601FAEAVNFCTVD4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
N601FAEAVNFAPID1Caenorhabditis elegans
N91RIQRLNELEAQ4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
N91RTQKLNEVEAI1Caenorhabditis elegans
P347PLHDVPKGDWR3Homo sapiens, Gallus gallus, Mus musculus
P347VLDEVPEGEWR1Caenorhabditis elegans
P347PLTDVPKGDWR1Danio rerio
S317CLLCGSGNDED3Homo sapiens, Gallus gallus, Mus musculus
S317CVACNEGKDED1Caenorhabditis elegans
S317CLVCGKGNDED1Danio rerio
S507DHWSYSINYLH4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
S507DHWTYSVNYNH1Caenorhabditis elegans
T416WRLVSTIEEDV3Homo sapiens, Gallus gallus, Mus musculus
T416WKNVISHENPV1Caenorhabditis elegans
T416WRLVGTIQEDV1Danio rerio
V307KATNAVDLYVC1Homo sapiens
V307DDEDPMDQVFC1Caenorhabditis elegans
V307PPVSMVDLYVC1Danio rerio
V307KPTSAVDLYVC1Gallus gallus
V307KTATAVDLYVC1Mus musculus
V311AVDLYVCLLCG3Homo sapiens, Gallus gallus, Mus musculus
V311PMDQVFCVACN1Caenorhabditis elegans
V311MVDLYVCLVCG1Danio rerio
V346PPLHDVPKGDW3Homo sapiens, Gallus gallus, Mus musculus
V346PVLDEVPEGEW1Caenorhabditis elegans
V346PPLTDVPKGDW1Danio rerio
V414EFWRLVSTIEE3Homo sapiens, Gallus gallus, Mus musculus
V414SFWKNVISHEN1Caenorhabditis elegans
V414EFWRLVGTIQE1Danio rerio
V600NFAEAVNFCTV4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
V600NFAEAVNFAPI1Caenorhabditis elegans
W351VPKGDWRCPKC3Homo sapiens, Danio rerio, Mus musculus
W351VPEGEWRCPKC1Caenorhabditis elegans
W351VPKGDWRCPQC1Gallus gallus
W486GMKLPWLYVGM3Homo sapiens, Gallus gallus, Mus musculus
W486GMMVPWVYVGM1Caenorhabditis elegans
W486GMTLPWLYVGM1Danio rerio
W519GEPKTWYGVPG2Homo sapiens, Mus musculus
W519GEPKTWYGAPG2Danio rerio, Gallus gallus
W519GERKIWYGVGG1Caenorhabditis elegans
Y310NAVDLYVCLLC1Homo sapiens
Y310DPMDQVFCVAC1Caenorhabditis elegans
Y310SMVDLYVCLVC1Danio rerio
Y310SAVDLYVCLLC1Gallus gallus
Y310TAVDLYVCLLC1Mus musculus
Y425DVTVEYGADIA4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
Y425PVSVKYGADLI1Caenorhabditis elegans
Y488KLPWLYVGMCF3Homo sapiens, Gallus gallus, Mus musculus
Y488MVPWVYVGMCF1Caenorhabditis elegans
Y488TLPWLYVGMCF1Danio rerio

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