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 KDM5D
Gene summary
Basic gene Info.Gene symbolKDM5D
Gene namelysine (K)-specific demethylase 5D
CytomapUCSC genome browser: Yq11
Type of geneprotein-coding
DescriptionH-YJumonji, AT rich interactive domain 1D (RBP2-like)SMC homolog, Y chromosomeSmcy homolog, Y-linkedhistocompatibility Y antigenhistone demethylase JARID1Djumonji/ARID domain-containing protein 1Dlysine-specific demethylase 5Dprotein SmcYselected
Modification date20141207
dbXrefs MIM : 426000
Ensembl : ENSG00000012817
Ensembl : ENSG00000278871
Ensembl : ENSG00000280101
Ensembl : ENSG00000280358
HPRD : 02464
Vega : OTTHUMG00000036508
ProteinUniProt: Q9BY66
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM5D
BioGPS: 8284
PathwayNCI Pathway Interaction Database: KDM5D
Pathway Commons: KDM5D
ContextiHOP: KDM5D
ligand binding site mutation search in PubMed: KDM5D
UCL Cancer Institute: KDM5D
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0034720histone H3-K4 demethylation17320160

Ligand binding site mutations for KDM5D
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 KDM5D
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 KDM5D from PDB

Differential gene expression and gene-gene network for KDM5D
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 KDM5D and the right PPI network was created from samples without mutations in the LBS of KDM5D. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for KDM5D
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for KDM5D
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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
Approved|nutraceuticalDB00126Vitamin CSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of KDM5D go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of KDM5D
Multiple alignments for Q9BY66 in multiple species
LBSAA sequence# speciesSpecies
C317IDSYICQVCSR2Homo sapiens, Pan troglodytes
C317MNSYVCRICSR1Mus musculus
C320YICQVCSRGDE2Homo sapiens, Pan troglodytes
C320YVCRICSRGDE1Mus musculus
C332DKLLFCDGCDD2Homo sapiens, Pan troglodytes
C332DKFLLCDGCSD1Mus musculus
C335LFCDGCDDNYH2Homo sapiens, Pan troglodytes
C335LLCDGCSDNYH1Mus musculus
C343NYHIFCLLPPL3Homo sapiens, Mus musculus, Pan troglodytes
C358RGIWRCPKCIL2Homo sapiens, Pan troglodytes
C358KGVWRCPKCIL1Mus musculus
C361WRCPKCILAEC3Homo sapiens, Mus musculus, Pan troglodytes
H340CDDNYHIFCLL2Homo sapiens, Pan troglodytes
H340CSDNYHIFCLL1Mus musculus

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