mutLBSgeneDB

mutLBSgeneDB
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 KDM4D
Gene summary
Basic gene Info.Gene symbolKDM4D
Gene namelysine (K)-specific demethylase 4D
SynonymsJMJD2D
CytomapUCSC genome browser: 11q21
Type of geneprotein-coding
RefGenesNM_018039.2,
DescriptionjmjC domain-containing histone demethylation protein 3Djumonji domain containing 2Djumonji domain-containing protein 2Dlysine-specific demethylase 4D
Modification date20141207
dbXrefs MIM : 609766
HGNC : HGNC
Ensembl : ENSG00000186280
HPRD : 17169
Vega : OTTHUMG00000167838
ProteinUniProt: Q6B0I6
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM4D
BioGPS: 55693
PathwayNCI Pathway Interaction Database: KDM4D
KEGG: KDM4D
REACTOME: KDM4D
Pathway Commons: KDM4D
ContextiHOP: KDM4D
ligand binding site mutation search in PubMed: KDM4D
UCL Cancer Institute: KDM4D
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0033169histone H3-K9 demethylation25124442


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Ligand binding site mutations for KDM4D
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
I259,K255N257KCOAD1
A190A190VGBM1
Y89,T87Q88RKIRC1
R316R316WLUAD1
P260P260HLUAD1
C312G313VLUAD1
P232P232SSKCM1
P260P260SSKCM1
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.


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Protein structure related information for KDM4D
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
P260P260S-1.1111553
P260P260H-1.1039586
K255N257K-0.88944725
I259N257K-0.88944725
P232P232S-0.86007129
A190A190V-0.80837138
R316R316W-0.78017746
C312G313V-0.53003998
Y89Q88R-0.48188855
T87Q88R-0.48188855
(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 KDM4D from PDB

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Differential gene expression and gene-gene network for KDM4D
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 KDM4D and the right PPI network was created from samples without mutations in the LBS of KDM4D. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for KDM4D
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for KDM4D
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 KDM4D go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
PDOPROPANE-1,3-DIOL4honAA190
ZNZINC(2+)3dxtAC312
ZNZINC(2+)3dxuAC312
ZNZINC(2+)4honAC312
ZNZINC(2+)4honBC312
ZNZINC(2+)4hooAC312
ZNZINC(2+)4hooBC312
ZNZINC(2+)4d6qAC312
ZNZINC(2+)4d6rAC312
ZNZINC(2+)4d6sAC312
ZNZINC(2+)5f5aAC312
ZNZINC(2+)5f5cAC312
IEJO-TOLUENESULFONAMIDE4d6rAK255 I259 P260
PDOPROPANE-1,3-DIOL4honAT87 Y89 P232
IIIPeptide ligand (THR,ALA,ARG,LYS,SER,THR,GLY,GLY,LYS,ALA)4honAY89 R316
IIIPeptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY)4honBY89 R316


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Conservation information for LBS of KDM4D
Multiple alignments for Q6B0I6 in multiple species
LBSAA sequence# speciesSpecies
A138SPIYGADVSGS3Mus musculus, Rattus norvegicus, Rattus norvegicus
A138SPIYGADISGS1Homo sapiens
A190WKTTFAWHTED2Homo sapiens, Mus musculus
A190WKTSFAWHTED2Rattus norvegicus, Rattus norvegicus
A292FNCAEAINFAT4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
C238GSSQGCQAFLR3Mus musculus, Rattus norvegicus, Rattus norvegicus
C238GSSRGCGAFLR1Homo sapiens
C310KVASQCSCGEA3Mus musculus, Rattus norvegicus, Rattus norvegicus
C310KMASQCSCGEA1Homo sapiens
C312ASQCSCGEARV4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
D139PIYGADVSGSL3Mus musculus, Rattus norvegicus, Rattus norvegicus
D139PIYGADISGSL1Homo sapiens
E173CGIVIEGVNTP3Mus musculus, Rattus norvegicus, Rattus norvegicus
E173CGVVIEGVNTP1Homo sapiens
E194FAWHTEDMDLY4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
E56VIPPKEWRARQ3Mus musculus, Rattus norvegicus, Rattus norvegicus
E56IIPPKEWKARE1Homo sapiens
F189MWKTTFAWHTE2Homo sapiens, Mus musculus
F189MWKTSFAWHTE2Rattus norvegicus, Rattus norvegicus
F231LAKELFPGSSQ2Rattus norvegicus, Rattus norvegicus
F231LARELFPGSSR1Homo sapiens
F231LARELFPGSSQ1Mus musculus
F261ENGIPFGRITQ3Mus musculus, Rattus norvegicus, Rattus norvegicus
F261ENGIPFNRITQ1Homo sapiens
F28PTKEEFNDFDK4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
G142GADVSGSLFDG3Mus musculus, Rattus norvegicus, Rattus norvegicus
G142GADISGSLFDE1Homo sapiens
G174GIVIEGVNTPY3Mus musculus, Rattus norvegicus, Rattus norvegicus
G174GVVIEGVNTPY1Homo sapiens
H192TTFAWHTEDMD2Homo sapiens, Mus musculus
H192TSFAWHTEDMD2Rattus norvegicus, Rattus norvegicus
H244QAFLRHKVALI3Mus musculus, Rattus norvegicus, Rattus norvegicus
H244GAFLRHKVALI1Homo sapiens
H280FPYGYHAGFNH4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
H90VFTQYHKKKKA3Homo sapiens, Rattus norvegicus, Rattus norvegicus
H90VFTQYHKKKKG1Mus musculus
I140IYGADVSGSLF3Mus musculus, Rattus norvegicus, Rattus norvegicus
I140IYGADISGSLF1Homo sapiens
I20NCSIMIFRPTK3Mus musculus, Rattus norvegicus, Rattus norvegicus
I20NCNIMIFHPTK1Homo sapiens
I259LKENGIPFGRI3Mus musculus, Rattus norvegicus, Rattus norvegicus
I259LKENGIPFNRI1Homo sapiens
I293NCAEAINFATP4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
I69DNISNILIATP3Mus musculus, Rattus norvegicus, Rattus norvegicus
I69DNISEILIATP1Homo sapiens
K210HFGQPKTWYAV3Mus musculus, Rattus norvegicus, Rattus norvegicus
K210HLGEPKTWYVV1Homo sapiens
K245AFLRHKVALIS4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
K25IFRPTKEEFND3Mus musculus, Rattus norvegicus, Rattus norvegicus
K25IFHPTKEEFND1Homo sapiens
K255SPTVLKENGIP4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
L180VNTPYLYFGMW4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
M19PNCSIMIFRPT3Mus musculus, Rattus norvegicus, Rattus norvegicus
M19PNCNIMIFHPT1Homo sapiens
M306IDYGKVASQCS3Mus musculus, Rattus norvegicus, Rattus norvegicus
M306IDYGKMASQCS1Homo sapiens
N202DLYSINYLHFG3Mus musculus, Rattus norvegicus, Rattus norvegicus
N202DLYSINYLHLG1Homo sapiens
N29TKEEFNDFDKY4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
N294CAEAINFATPR4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
P232AKELFPGSSQG2Rattus norvegicus, Rattus norvegicus
P232ARELFPGSSRG1Homo sapiens
P232ARELFPGSSQG1Mus musculus
P260KENGIPFGRIT3Mus musculus, Rattus norvegicus, Rattus norvegicus
P260KENGIPFNRIT1Homo sapiens
P54AKVIPPKEWRA3Mus musculus, Rattus norvegicus, Rattus norvegicus
P54AKIIPPKEWKA1Homo sapiens
Q151DGKTQQWNVGH3Mus musculus, Rattus norvegicus, Rattus norvegicus
Q151DENTKQWNLGH1Homo sapiens
Q221PPEHGRRLELL2Rattus norvegicus, Rattus norvegicus
Q221PPEHGQRLERL1Homo sapiens
Q221PPEHGRRLERL1Mus musculus
R316SCGEARVSFSM3Mus musculus, Rattus norvegicus, Rattus norvegicus
R316SCGEARVTFSM1Homo sapiens
S141YGADVSGSLFD3Mus musculus, Rattus norvegicus, Rattus norvegicus
S141YGADISGSLFD1Homo sapiens
S143ADVSGSLFDGK3Mus musculus, Rattus norvegicus, Rattus norvegicus
S143ADISGSLFDEN1Homo sapiens
S200DMDLYSINYLH4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
T87QAGVFTQYHKK3Mus musculus, Rattus norvegicus, Rattus norvegicus
T87RAGVFTQYHKK1Homo sapiens
V317CGEARVSFSMD3Mus musculus, Rattus norvegicus, Rattus norvegicus
V317CGEARVTFSMD1Homo sapiens
W212GQPKTWYAVPP3Mus musculus, Rattus norvegicus, Rattus norvegicus
W212GEPKTWYVVPP1Homo sapiens
W57IPPKEWRARQS3Mus musculus, Rattus norvegicus, Rattus norvegicus
W57IPPKEWKARET1Homo sapiens
Y136YESPIYGADVS3Mus musculus, Rattus norvegicus, Rattus norvegicus
Y136YNSPIYGADIS1Homo sapiens
Y179GVNTPYLYFGM4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
Y181NTPYLYFGMWK4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
Y277MVTFPYGYHAG4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus
Y303PRWIDYGKVAS3Mus musculus, Rattus norvegicus, Rattus norvegicus
Y303PRWIDYGKMAS1Homo sapiens
Y89GVFTQYHKKKK4Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus


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