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 KDM4A
Gene summary
Basic gene Info.Gene symbolKDM4A
Gene namelysine (K)-specific demethylase 4A
CytomapUCSC genome browser: 1p34.1
Type of geneprotein-coding
DescriptionjmjC domain-containing histone demethylation protein 3Ajumonji C domain-containing histone demethylase 3Ajumonji domain containing 2jumonji domain containing 2Ajumonji domain-containing protein 2Alysine-specific demethylase 4Atudor domain containing
Modification date20141207
dbXrefs MIM : 609764
Ensembl : ENSG00000066135
HPRD : 17168
Vega : OTTHUMG00000007560
ProteinUniProt: O75164
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM4A
BioGPS: 9682
PathwayNCI Pathway Interaction Database: KDM4A
Pathway Commons: KDM4A
ContextiHOP: KDM4A
ligand binding site mutation search in PubMed: KDM4A
UCL Cancer Institute: KDM4A
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0016577histone demethylation16024779
GO:0045892negative regulation of transcription, DNA-templated16024779
GO:0070544histone H3-K36 demethylation16024779

Ligand binding site mutations for KDM4A
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 KDM4A
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 KDM4A from PDB

Differential gene expression and gene-gene network for KDM4A
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 KDM4A and the right PPI network was created from samples without mutations in the LBS of KDM4A. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for KDM4A
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for KDM4A
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 KDM4A go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (THR,GLY,GLY,VAL,LYS,LYS)2pxjBI166 I168 Y175 K314
IIIPeptide ligand (THR,GLY,GLY,VAL,LYS)2q8dBI166 I168 Y175 K314
IIIPeptide ligand (THR,ALA,ARG,LYS,SER,THR,GLY,GLY)2q8cBI168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,CYS,GLY,GLY,LYS)3u4sAI168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,CYS,GLY)3u4sBI168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,ALA)4v2vAI168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,ALA)4v2vBI168 Y175
IIIPeptide ligand (GLY,GLY,VAL,LYS,LYS)2pxjAI168 Y175 K314
IIIPeptide ligand (GLY,GLY,VAL,LYS)2q8dAI168 Y175 K314
IIIPeptide ligand (GLY,GLY,VAL,LYS)2q8eAI168 Y175 K314
IIIPeptide ligand (GLY,GLY,VAL,LYS,LYS,PRO,HIS)2q8eBI168 Y175 K314
IIIPeptide ligand (SER,THR,GLY,GLY,VAL,LYS,LYS,PRO,HIS,ARG,TYR)2os2AI87 I166 I168 Y175 K314
IIIPeptide ligand (SER,THR,GLY,GLY,VAL,LYS,LYS,PRO,HIS,ARG,TYR)2os2BI87 I166 I168 Y175 K314
IIIPeptide ligand (PRO,ALA,THR,GLY,GLY,VAL,LYS,LYS,PRO,HIS,ARG,TYR)2ybpAI87 I166 I168 Y175 K314
IIIPeptide ligand (PRO,ALA,THR,GLY,GLY,VAL,LYS,LYS,PRO,HIS,ARG,TYR)2ybpBI87 I166 I168 Y175 K314
IIIPeptide ligand (PRO,ALA,THR,GLY,GLY,VAL,LYS,LYS,PRO,HIS,ARG,TYR)2ybsAI87 I166 I168 Y175 K314
IIIPeptide ligand (PRO,ALA,THR,GLY,GLY,VAL,LYS,LYS,PRO,HIS,ARG,TYR)2ybsBI87 I166 I168 Y175 K314
IIIPeptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY,LYS)2oq6AI87 I168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY,LYS)2oq6BI87 I168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY,LYS)2ot7AI87 I168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY,LYS)2ox0AI87 I168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY,LYS)2ox0BI87 I168 Y175
IIIPeptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY,LYS)2ot7BI87 Y175
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA)2gfaAN940 Y942
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA)2gfaBN940 Y942
IIIPeptide ligand (ALA,ARG,LYS,SER)2q8cAY175
IIIPeptide ligand (ALA,ARG,LYS,SER)4v2wAY175

Conservation information for LBS of KDM4A
Multiple alignments for O75164 in multiple species
LBSAA sequence# speciesSpecies
A134PPIYGADVNGT2Homo sapiens, Mus musculus
A134EPIYGADTEGS1Caenorhabditis elegans
A69DLVIPAPIQQL2Homo sapiens, Mus musculus
A69DYEITQPARET1Caenorhabditis elegans
C234GSAQSCEAFLR2Homo sapiens, Mus musculus
C234EYAPQCKAFLR1Caenorhabditis elegans
C306KQAVLCSCRKD2Homo sapiens, Mus musculus
C306KDAVLCDCNKD1Caenorhabditis elegans
C308AVLCSCRKDMV2Homo sapiens, Mus musculus
C308AVLCDCNKDSV1Caenorhabditis elegans
D135PIYGADVNGTL2Homo sapiens, Mus musculus
D135PIYGADTEGSF1Caenorhabditis elegans
D191AWHTEDMDLYS2Homo sapiens, Mus musculus
D191PWHAEDMDLYS1Caenorhabditis elegans
D311CSCRKDMVKIS2Homo sapiens, Mus musculus
D311CDCNKDSVKID1Caenorhabditis elegans
D934EVNFDDGSFSD2Homo sapiens, Mus musculus
D934VVDFLDNSCSR1Caenorhabditis elegans
D939DGSFSDNLYPE2Homo sapiens, Mus musculus
D939DNSCSRDNHVE1Caenorhabditis elegans
D969QVRWTDGQVYG2Homo sapiens, Mus musculus
D969KVVWDDKQVYD1Caenorhabditis elegans
E169SGITIEGVNTP2Homo sapiens, Mus musculus
E169TNYEIKGVNTV1Caenorhabditis elegans
E190FAWHTEDMDLY2Homo sapiens, Mus musculus
E190FPWHAEDMDLY1Caenorhabditis elegans
E23YPTMEEFRNFS2Homo sapiens, Mus musculus
E23YPTMREFKNFS1Caenorhabditis elegans
F185MWKTSFAWHTE2Homo sapiens, Mus musculus
F185MYKTTFPWHAE1Caenorhabditis elegans
F353PEAAEFLKES-1Homo sapiens
F353PKKK-------1Caenorhabditis elegans
F353PEAAEFLKDSG1Mus musculus
F932FYEVNFDDGSF2Homo sapiens, Mus musculus
F932TVVVDFLDNSC1Caenorhabditis elegans
F937FDDGSFSDNLY2Homo sapiens, Mus musculus
F937FLDNSCSRDNH1Caenorhabditis elegans
G170GITIEGVNTPY2Homo sapiens, Mus musculus
G170NYEIKGVNTVY1Caenorhabditis elegans
G935VNFDDGSFSDN2Homo sapiens, Mus musculus
G935VDFLDNSCSRD1Caenorhabditis elegans
H188TSFAWHTEDMD2Homo sapiens, Mus musculus
H188TTFPWHAEDMD1Caenorhabditis elegans
H240EAFLRHKMTLI2Homo sapiens, Mus musculus
H240KAFLRHKTYLV1Caenorhabditis elegans
H276FPYGYHAGFNH2Homo sapiens, Mus musculus
H276FPRGYHMGFNL1Caenorhabditis elegans
I166EKESGITIEGV2Homo sapiens, Mus musculus
I166--DTNYEIKGV1Caenorhabditis elegans
I168ESGITIEGVNT2Homo sapiens, Mus musculus
I168DTNYEIKGVNT1Caenorhabditis elegans
I315KDMVKISMDVF2Homo sapiens, Mus musculus
I315KDSVKIDMTHF1Caenorhabditis elegans
I71VIPAPIQQLV-2Homo sapiens, Mus musculus
I71EITQPARETIE1Caenorhabditis elegans
I87FTQYNIQ-KKA2Homo sapiens, Mus musculus
I87YFKRNVTCRRK1Caenorhabditis elegans
K206HFGEPKSWYSV2Homo sapiens, Mus musculus
K206HFGAPKYWFAI1Caenorhabditis elegans
K241AFLRHKMTLIS2Homo sapiens, Mus musculus
K241AFLRHKTYLVT1Caenorhabditis elegans
K310LCSCRKDMVKI2Homo sapiens, Mus musculus
K310LCDCNKDSVKI1Caenorhabditis elegans
K314RKDMVKISMDV2Homo sapiens, Mus musculus
K314NKDSVKIDMTH1Caenorhabditis elegans
M242FLRHKMTLISP2Homo sapiens, Mus musculus
M242FLRHKTYLVTP1Caenorhabditis elegans
M312SCRKDMVKISM2Homo sapiens, Mus musculus
M312DCNKDSVKIDM1Caenorhabditis elegans
N137YGADVNGTLYE2Homo sapiens, Mus musculus
N137YGADTEGSFYD1Caenorhabditis elegans
N198DLYSINYLHFG2Homo sapiens, Mus musculus
N198DLYSINFLHFG1Caenorhabditis elegans
N290CAESTNFATRR2Homo sapiens, Mus musculus
N290LAESTNFASQR1Caenorhabditis elegans
N86LFTQYNIQ-KK2Homo sapiens, Mus musculus
N86AYFKRNVTCRR1Caenorhabditis elegans
N931TFYEVNFDDGS2Homo sapiens, Mus musculus
N931ETVVVDFLDNS1Caenorhabditis elegans
N940GSFSDNLYPED2Homo sapiens, Mus musculus
N940NSCSRDNHVED1Caenorhabditis elegans
Q84SGLFTQYNIQ-2Homo sapiens, Mus musculus
Q84PGAYFKRNVTC1Caenorhabditis elegans
Q88TQYNIQ-KKAM2Homo sapiens, Mus musculus
Q88FKRNVTCRRKM1Caenorhabditis elegans
R309VLCSCRKDMVK2Homo sapiens, Mus musculus
R309VLCDCNKDSVK1Caenorhabditis elegans
S196DMDLYSINYLH2Homo sapiens, Mus musculus
S196DMDLYSINFLH1Caenorhabditis elegans
S288FNCAESTNFAT2Homo sapiens, Mus musculus
S288YNLAESTNFAS1Caenorhabditis elegans
S316DMVKISMDVFV2Homo sapiens, Mus musculus
S316DSVKIDMTHFM1Caenorhabditis elegans
S936NFDDGSFSDNL2Homo sapiens, Mus musculus
S936DFLDNSCSRDN1Caenorhabditis elegans
S938DDGSFSDNLYP2Homo sapiens, Mus musculus
S938LDNSCSRDNHV1Caenorhabditis elegans
T270GEFMITFPYGY2Homo sapiens, Mus musculus
T270NEFIITFPRGY1Caenorhabditis elegans
T289NCAESTNFATR2Homo sapiens, Mus musculus
T289NLAESTNFASQ1Caenorhabditis elegans
T968VQVRWTDGQVY2Homo sapiens, Mus musculus
T968VKVVWDDKQVY1Caenorhabditis elegans
V160TILDLVEKESG2Homo sapiens, Mus musculus
V160TILE----DTN1Caenorhabditis elegans
V171ITIEGVNTPYL2Homo sapiens, Mus musculus
V171YEIKGVNTVYL1Caenorhabditis elegans
V313CRKDMVKISMD2Homo sapiens, Mus musculus
V313CNKDSVKIDMT1Caenorhabditis elegans
W208GEPKSWYSVPP2Homo sapiens, Mus musculus
W208GAPKYWFAISS1Caenorhabditis elegans
W967VVQVRWTDGQV2Homo sapiens, Mus musculus
W967RVKVVWDDKQV1Caenorhabditis elegans
Y132FNPPIYGADVN2Homo sapiens, Mus musculus
Y132HGEPIYGADTE1Caenorhabditis elegans
Y175GVNTPYLYFGM2Homo sapiens, Mus musculus
Y175GVNTVYLYFGM1Caenorhabditis elegans
Y177NTPYLYFGMWK2Homo sapiens, Mus musculus
Y177NTVYLYFGMYK1Caenorhabditis elegans
Y33SRYIAYIESQG2Homo sapiens, Mus musculus
Y33SQYIKKIEQNG1Caenorhabditis elegans
Y85GLFTQYNIQ-K2Homo sapiens, Mus musculus
Y85GAYFKRNVTCR1Caenorhabditis elegans
Y942FSDNLYPEDIV2Homo sapiens, Mus musculus
Y942CSRDNHVEDII1Caenorhabditis elegans
Y973TDGQVYGAKFV2Homo sapiens, Mus musculus
Y973DDKQVYDAYFR1Caenorhabditis elegans

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