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 PDK3
Gene summary
Basic gene Info.Gene symbolPDK3
Gene namepyruvate dehydrogenase kinase, isozyme 3
CytomapUCSC genome browser: Xp22.11
Type of geneprotein-coding
Description[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrialpyruvate dehydrogenase kinase, isoenzyme 3pyruvate dehydrogenase, lipoamide, kinase isozyme 3, mitochondrial
Modification date20141207
dbXrefs MIM : 300906
Ensembl : ENSG00000067992
HPRD : 03956
Vega : OTTHUMG00000021269
ProteinUniProt: Q15120
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDK3
BioGPS: 5165
PathwayNCI Pathway Interaction Database: PDK3
Pathway Commons: PDK3
ContextiHOP: PDK3
ligand binding site mutation search in PubMed: PDK3
UCL Cancer Institute: PDK3
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0018105peptidyl-serine phosphorylation11486000

Ligand binding site mutations for PDK3
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 PDK3
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 PDK3 from PDB

Differential gene expression and gene-gene network for PDK3
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 PDK3 and the right PPI network was created from samples without mutations in the LBS of PDK3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PDK3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for PDK3
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
ExperimentalDB03758RadicicolSmall molecule
ExperimentalDB03760Dihydrolipoic AcidSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PDK3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ADPADP1y8oAD287 L300 F324
ATPATP1y8pAD287 L300 F324

Conservation information for LBS of PDK3
Multiple alignments for Q15120 in multiple species
LBSAA sequence# speciesSpecies
A255KNSMRATVELY1Homo sapiens
A255KNSLRATVEFH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A255KNSLRAVQERF1Arabidopsis thaliana
A255KNAMRATVEYH1Caenorhabditis elegans
A255KNSMRATVELH1Mus musculus
A322RAAPLAGFGYG2Homo sapiens, Mus musculus
A322STTPMAGFGFG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A322VPVTMAGYGYG1Arabidopsis thaliana
A322-QAPLAGYGYG1Caenorhabditis elegans
A399SEPRDASKYKA2Homo sapiens, Mus musculus
A399-----------2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana
A399QGNRPAQS---1Caenorhabditis elegans
D287SIKISDLGGGV2Homo sapiens, Mus musculus
D287TIKISDEGGGI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D287TIKVSDEGGGI1Arabidopsis thaliana
D287SIKICDRGGGV1Caenorhabditis elegans
E247FHMLFELFKNS2Homo sapiens, Mus musculus
E247NHAVFEILKNS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E247HLMMYELVKNS1Arabidopsis thaliana
E247YHMMFELFKNA1Caenorhabditis elegans
F32LSIKQFLDFGR2Homo sapiens, Mus musculus
F32LSLKQLVYFGK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F32VSLRYMMEFGS1Arabidopsis thaliana
F32LTIQQYLDFGR1Caenorhabditis elegans
F324APLAGFGYGLP2Homo sapiens, Mus musculus
F324TPMAGFGFGLP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F324VTMAGYGYGLP1Arabidopsis thaliana
F324APLAGYGYGLP1Caenorhabditis elegans
F35KQFLDFGRDNA2Homo sapiens, Mus musculus
F35KQLVYFGKNPT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F35RYMMEFGSKPT1Arabidopsis thaliana
F35QQYLDFGRIGT1Caenorhabditis elegans
F48-TSYMFLRKEL2Homo sapiens, Mus musculus
F48FRAGLFLRDEL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F48LISAQFLHKEL1Arabidopsis thaliana
F48--SYTFLKNEL1Caenorhabditis elegans
G323AAPLAGFGYGL2Homo sapiens, Mus musculus
G323TTPMAGFGFGL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G323PVTMAGYGYGL1Arabidopsis thaliana
G323QAPLAGYGYGL1Caenorhabditis elegans
G325PLAGFGYGLPI2Homo sapiens, Mus musculus
G325PMAGFGFGLPL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G325TMAGYGYGLPI1Arabidopsis thaliana
G325PLAGYGYGLPL1Caenorhabditis elegans
G327AGFGYGLPISR2Homo sapiens, Mus musculus
G327AGFGFGLPLAR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G327AGYGYGLPISR1Arabidopsis thaliana
G327AGYGYGLPLSR1Caenorhabditis elegans
K250LFELFKNSMRA2Homo sapiens, Mus musculus
K250VFEILKNSLRA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K250MYELVKNSLRA1Arabidopsis thaliana
K250MFELFKNAMRA1Caenorhabditis elegans
L248HMLFELFKNSM2Homo sapiens, Mus musculus
L248HAVFEILKNSL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L248LMMYELVKNSL1Arabidopsis thaliana
L248HMMFELFKNAM1Caenorhabditis elegans
L27FSPSPLSIKQF2Homo sapiens, Mus musculus
L27YPQTGLSLKQL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L27MKQTGVSLRYM1Arabidopsis thaliana
L27FQPSSLTIQQY1Caenorhabditis elegans
L300RKIDRLFNYMY2Homo sapiens, Mus musculus
L300RNIPLVWSYMF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L300SGLPRIFTYLY1Arabidopsis thaliana
L300TILERLYNYMY1Caenorhabditis elegans
L328GFGYGLPISRL2Homo sapiens, Mus musculus
L328GFGFGLPLARL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L328GYGYGLPISRL1Arabidopsis thaliana
L328GYGYGLPLSRL1Caenorhabditis elegans
L49TSYMFLRKELP2Homo sapiens, Mus musculus
L49RAGLFLRDELP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L49ISAQFLHKELP1Arabidopsis thaliana
L49-SYTFLKNELL1Caenorhabditis elegans
N251FELFKNSMRAT2Homo sapiens, Mus musculus
N251FEILKNSLRAT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N251YELVKNSLRAV1Arabidopsis thaliana
N251FELFKNAMRAT1Caenorhabditis elegans
Q31PLSIKQFLDFG2Homo sapiens, Mus musculus
Q31GLSLKQLVYFG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q31GVSLRYMMEFG1Arabidopsis thaliana
Q31SLTIQQYLDFG1Caenorhabditis elegans
R254FKNSMRATVEL2Homo sapiens, Mus musculus
R254LKNSLRATVEF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R254VKNSLRAVQER1Arabidopsis thaliana
R254FKNAMRATVEY1Caenorhabditis elegans
R397PSSEPRDASKY2Homo sapiens, Mus musculus
R397-----------2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana
R397PGQGNRPAQS-1Caenorhabditis elegans
S252ELFKNSMRATV2Homo sapiens, Mus musculus
S252EILKNSLRATV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S252ELVKNSLRAVQ1Arabidopsis thaliana
S252ELFKNAMRATV1Caenorhabditis elegans
S306FNYMYSTAPRP2Homo sapiens, Mus musculus
S306WSYMFTTASPT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S306FTYLYSTARNP1Arabidopsis thaliana
S306YNYMYSTAPPP1Caenorhabditis elegans
S45EK--TSYMFLR2Homo sapiens, Mus musculus
S45GTLFRAGLFLR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S45RNLLISAQFLH1Arabidopsis thaliana
S45AN---SYTFLK1Caenorhabditis elegans
T307NYMYSTAPRPS2Homo sapiens, Mus musculus
T307SYMFTTASPTL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T307TYLYSTARNPL1Arabidopsis thaliana
T307NYMYSTAPPPP1Caenorhabditis elegans
T352MEGVGTDAVIY2Homo sapiens, Mus musculus
T352MEGYGTDVYIH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T352MEGYGTDAYLH1Arabidopsis thaliana
T352MEGHGTDACIY1Caenorhabditis elegans
V292DLGGGVPLRKI2Homo sapiens, Mus musculus
V292DEGGGISRRNI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V292DEGGGIARSGL1Arabidopsis thaliana
V292DRGGGVSRTIL1Caenorhabditis elegans
Y305LFNYMYSTAPR2Homo sapiens, Mus musculus
Y305VWSYMFTTASP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y305IFTYLYSTARN1Arabidopsis thaliana
Y305LYNYMYSTAPP1Caenorhabditis elegans
Y326LAGFGYGLPIS2Homo sapiens, Mus musculus
Y326MAGFGFGLPLA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y326MAGYGYGLPIS1Arabidopsis thaliana
Y326LAGYGYGLPLS1Caenorhabditis elegans

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