mutLBSgeneDB |
Gene summary for PDK2 |
Gene summary |
Basic gene Info. | Gene symbol | PDK2 |
Gene name | pyruvate dehydrogenase kinase, isozyme 2 | |
Synonyms | PDHK2|PDKII | |
Cytomap | UCSC genome browser: 17q21.33 | |
Type of gene | protein-coding | |
RefGenes | NM_001199898.1, NM_001199899.1,NM_001199900.1,NM_002611.4, | |
Description | PDH kinase 2[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrialpyruvate dehydrogenase kinase, isoenzyme 2pyruvate dehydrogenase, lipoamide, kinase isozyme 2, mitochondrial | |
Modification date | 20141207 | |
dbXrefs | MIM : 602525 | |
HGNC : HGNC | ||
Ensembl : ENSG00000005882 | ||
HPRD : 03955 | ||
Vega : OTTHUMG00000161948 | ||
Protein | UniProt: Q15119 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PDK2 | |
BioGPS: 5164 | ||
Pathway | NCI Pathway Interaction Database: PDK2 | |
KEGG: PDK2 | ||
REACTOME: PDK2 | ||
Pathway Commons: PDK2 | ||
Context | iHOP: PDK2 | |
ligand binding site mutation search in PubMed: PDK2 | ||
UCL Cancer Institute: PDK2 | ||
Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO Term | PubMed ID | GO:0006468 | protein phosphorylation | 19833728 |
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Ligand binding site mutations for PDK2 |
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 |
LBS | AAchange of nsSNV | Cancer type | # samples | R74 | R74Q | BRCA | 1 | A259 | A259V | COAD | 1 | M130 | M130I | KIRC | 1 | R162 | R162S | LUSC | 1 | V81 | P79L | SKCM | 1 |
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 PDK2 |
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. |
LBS | AAchange of nsSNV | Relative stability change | R74 | R74Q | -1.1841045 | R162 | R162S | -0.97468287 | M130 | M130I | -0.66688305 | V81 | P79L | -0.48079363 | A259 | A259V | -0.190975 |
(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 PDK2 from PDB |
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Differential gene expression and gene-gene network for PDK2 |
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) |
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Phenotype information for PDK2 |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0878544 | Cardiomyopathies | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for PDK2 |
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 status | DrugBank ID | Name | Type | Drug structure |
Experimental | DB08608 | 4-({(2R,5S)-2,5-DIMETHYL-4-[(2R)-3,3,3-TRIFLUORO-2-HYDROXY-2-METHYLPROPANOYL]PIPERAZIN-1-YL}CARBONYL)BENZONITRILE | Small molecule | |
Experimental | DB08609 | (N-{4-[(ETHYLANILINO)SULFONYL]-2-METHYLPHENYL}-3,3,3-TRIFLUORO-2-HYDROXY-2-METHYLPROPANAMIDE | Small molecule | |
Experimental | DB08610 | N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE | Small molecule |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of PDK2 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | PV1 | (5-BROMO-2,4-DIHYDROXYPHENYL)(1,3-DIHYDRO-2H-ISOINDOL- 2-YL)METHANONE | 4mp2 | A | A259 | PFT | 4-(1,3-DIHYDRO-2H-ISOINDOL-2-YLCARBONYL)BENZENE-1,3-DIOL | 4mp7 | A | A259 | PV2 | 4-(ISOINDOLIN-2-YLSULFONYL)BENZENE-1,3-DIOL | 4mpc | A | A259 | PV8 | 4-[(5-HYDROXY-1,3-DIHYDRO-2H-ISOINDOL-2-YL) SULFONYL]BENZENE-1,3-DIOL | 4mpe | A | A259 | PV0 | 2-[(2,4-DIHYDROXYPHENYL)SULFONYL]-2,3-DIHYDRO-1H- ISOINDOLE-4,6-DIOL | 4mpn | A | A259 |
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Conservation information for LBS of PDK2 |
Multiple alignments for Q15119 in multiple species |
LBS | AA sequence | # species | Species | A259 | KNAMRATVESH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A324 | GGTPLAGFGYG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D290 | SIKMSDRGGGV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E251 | YHMLFELFKNA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E262 | MRATVESHESS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F326 | TPLAGFGYGLP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F52 | KTSFTFLRQEL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G133 | PTMAQGVLEYK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G294 | SDRGGGVPLRK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G325 | GTPLAGFGYGL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G327 | PLAGFGYGLPI | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G329 | AGFGYGLPISR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H123 | TIRNRHNDVVP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I119 | DALVTIRNRHN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I151 | VSNQNIQYFLD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I165 | LSRISIRMLIN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I169 | SIRMLINQHTL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L155 | NIQYFLDRFYL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L168 | ISIRMLINQHT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L252 | HMLFELFKNAM | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L303 | RKIERLFSYMY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L31 | FSPSPLSMKQF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L323 | TGGTPLAGFGY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L330 | GFGYGLPISRL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L346 | QGDLQLFSMEG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L53 | TSFTFLRQELP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L61 | ELPVRLANIMK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L71 | KEINLLPDRVL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M130 | DVVPTMAQGVL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N150 | PVSNQNIQYFL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N255 | FELFKNAMRAT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | P331 | FGYGLPISRLY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | P72 | EINLLPDRVLS | 2 | Homo sapiens, Rattus norvegicus | P72 | EINLLPDRVLG | 1 | Mus musculus | Q171 | RMLINQHTLIF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Q35 | PLSMKQFLDFG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R120 | ALVTIRNRHND | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R162 | RFYLSRISIRM | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R166 | SRISIRMLINQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R258 | FKNAMRATVES | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R74 | NLLPDRVLSTP | 2 | Homo sapiens, Rattus norvegicus | R74 | NLLPDRVLGTP | 1 | Mus musculus | S49 | ACEKTSFTFLR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T354 | MEGFGTDAVIY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V134 | TMAQGVLEYKD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V295 | DRGGGVPLRKI | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V75 | LLPDRVLSTPS | 2 | Homo sapiens, Rattus norvegicus | V75 | LLPDRVLGTPS | 1 | Mus musculus | V81 | LSTPSVQLVQS | 2 | Homo sapiens, Rattus norvegicus | V81 | LGTPSVQLVQS | 1 | Mus musculus | Y137 | QGVLEYKDTYG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Y328 | LAGFGYGLPIS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Y382 | SAWRHYQTIQE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Y88 | LVQSWYVQSLL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus |
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