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 PDK4
Gene summary
Basic gene Info.Gene symbolPDK4
Gene namepyruvate dehydrogenase kinase, isozyme 4
CytomapUCSC genome browser: 7q21.3
Type of geneprotein-coding
Description[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4, mitochondrialpyruvate dehydrogenase kinase, isoenzyme 4pyruvate dehydrogenase, lipoamide, kinase isozyme 4, mitochondri
Modification date20141207
dbXrefs MIM : 602527
Ensembl : ENSG00000004799
HPRD : 03957
Vega : OTTHUMG00000153977
ProteinUniProt: Q16654
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDK4
BioGPS: 5166
PathwayNCI Pathway Interaction Database: PDK4
Pathway Commons: PDK4
ContextiHOP: PDK4
ligand binding site mutation search in PubMed: PDK4
UCL Cancer Institute: PDK4
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006468protein phosphorylation18658136
GO:0009267cellular response to starvation14966024

Ligand binding site mutations for PDK4
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 PDK4
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 PDK4 from PDB

Differential gene expression and gene-gene network for PDK4
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 PDK4 and the right PPI network was created from samples without mutations in the LBS of PDK4. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PDK4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0011853Diabetes Mellitus, Experimental1Biomarker
umls:C0151744Myocardial Ischemia1Biomarker

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

Pharmacological information for PDK4
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
ExperimentalDB083564-[4-(4-methoxyphenyl)-5-methyl-1H-pyrazol-3-yl]benzene-1,3-diolSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PDK4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ADPADP2zdyAD293 L306
ADPADP2zdyBD293 L306
ANPAMP-PNP2e0aAD293 L306 Y311
ADPADP2zkjAD293 L306 Y311
ADPADP2zkjBD293 L306 Y311
ADPADP3d2rAD293 L306 Y311
ADPADP3d2rBD293 L306 Y311
ANPAMP-PNP2e0aBD293 L306 Y311 P335

Conservation information for LBS of PDK4
Multiple alignments for Q16654 in multiple species
LBSAA sequence# speciesSpecies
A262KNAMRATVEHQ3Homo sapiens, Mus musculus, Rattus norvegicus
A328RNAPLAGFGYG3Homo sapiens, Mus musculus, Rattus norvegicus
D293TIKISDRGGGV3Homo sapiens, Mus musculus, Rattus norvegicus
E254HHMLFELFKNA3Homo sapiens, Mus musculus, Rattus norvegicus
F330APLAGFGYGLP3Homo sapiens, Mus musculus, Rattus norvegicus
G295KISDRGGGVPL3Homo sapiens, Mus musculus, Rattus norvegicus
G297SDRGGGVPLRI3Homo sapiens, Mus musculus, Rattus norvegicus
G329NAPLAGFGYGL3Homo sapiens, Mus musculus, Rattus norvegicus
G331PLAGFGYGLPI3Homo sapiens, Mus musculus, Rattus norvegicus
G333AGFGYGLPISR3Homo sapiens, Mus musculus, Rattus norvegicus
K257LFELFKNAMRA3Homo sapiens, Mus musculus, Rattus norvegicus
L255HMLFELFKNAM3Homo sapiens, Mus musculus, Rattus norvegicus
L306RITDRLFSYTY2Mus musculus, Rattus norvegicus
L306RIIDRLFSYTY1Homo sapiens
L334GFGYGLPISRL3Homo sapiens, Mus musculus, Rattus norvegicus
L350QGDLNLYSMSG2Mus musculus, Rattus norvegicus
L350QGDLNLYSLSG1Homo sapiens
N258FELFKNAMRAT3Homo sapiens, Mus musculus, Rattus norvegicus
P335FGYGLPISRLY3Homo sapiens, Mus musculus, Rattus norvegicus
R261FKNAMRATVEH3Homo sapiens, Mus musculus, Rattus norvegicus
S312FSYTYSTAPTP3Homo sapiens, Mus musculus, Rattus norvegicus
T313SYTYSTAPTPV3Homo sapiens, Mus musculus, Rattus norvegicus
T358MSGYGTDAIIY2Mus musculus, Rattus norvegicus
T358LSGYGTDAIIY1Homo sapiens
V298DRGGGVPLRIT2Mus musculus, Rattus norvegicus
V298DRGGGVPLRII1Homo sapiens
Y311LFSYTYSTAPT3Homo sapiens, Mus musculus, Rattus norvegicus
Y332LAGFGYGLPIS3Homo sapiens, Mus musculus, Rattus norvegicus

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