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mutLBSgeneDB |
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| Gene summary for PDK4 |
 Gene summary |
| Basic gene Info. | Gene symbol | PDK4 |
| Gene name | pyruvate dehydrogenase kinase, isozyme 4 | |
| Synonyms | - | |
| Cytomap | UCSC genome browser: 7q21.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_002612.3, | |
| 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 date | 20141207 | |
| dbXrefs | MIM : 602527 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000004799 | ||
| HPRD : 03957 | ||
| Vega : OTTHUMG00000153977 | ||
| Protein | UniProt: Q16654 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PDK4 | |
| BioGPS: 5166 | ||
| Pathway | NCI Pathway Interaction Database: PDK4 | |
| KEGG: PDK4 | ||
| REACTOME: PDK4 | ||
| Pathway Commons: PDK4 | ||
| Context | iHOP: PDK4 | |
| ligand binding site mutation search in PubMed: PDK4 | ||
| UCL Cancer Institute: PDK4 | ||
| 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 | 18658136 | GO:0009267 | cellular response to starvation | 14966024 |
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| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D293 | D293N | SKCM | 1 | Y311 | T310A | STAD | 1 | P335 | S337Y | UCEC | 1 | L306 | R305C | UCEC | 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 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 |
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| 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 | Y311 | T310A | -1.5689248 | L306 | R305C | -1.2846577 | D293 | D293N | -0.81319863 | P335 | S337Y | -0.48948399 |
| (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 |
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| 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) |
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| Phenotype information for PDK4 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0011853 | Diabetes Mellitus, Experimental | 1 | Biomarker |
| umls:C0151744 | Myocardial Ischemia | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| 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. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Experimental | DB08356 | 4-[4-(4-methoxyphenyl)-5-methyl-1H-pyrazol-3-yl]benzene-1,3-diol | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PDK4 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | P4A | 3-(2,4-DIHYDROXYPHENYL)-4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOLE | 2zdx | A | D293 L306 | P4A | 3-(2,4-DIHYDROXYPHENYL)-4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOLE | 2zdx | B | D293 L306 | ADP | ADP | 2zdy | A | D293 L306 | ADP | ADP | 2zdy | B | D293 L306 | ANP | AMP-PNP | 2e0a | A | D293 L306 Y311 | ADP | ADP | 2zkj | A | D293 L306 Y311 | ADP | ADP | 2zkj | B | D293 L306 Y311 | ADP | ADP | 3d2r | A | D293 L306 Y311 | ADP | ADP | 3d2r | B | D293 L306 Y311 | ANP | AMP-PNP | 2e0a | B | D293 L306 Y311 P335 |
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| Conservation information for LBS of PDK4 |
| Multiple alignments for Q16654 in multiple species |
| LBS | AA sequence | # species | Species | A262 | KNAMRATVEHQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A328 | RNAPLAGFGYG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D293 | TIKISDRGGGV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E254 | HHMLFELFKNA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F330 | APLAGFGYGLP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G295 | KISDRGGGVPL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G297 | SDRGGGVPLRI | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G329 | NAPLAGFGYGL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G331 | PLAGFGYGLPI | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G333 | AGFGYGLPISR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K257 | LFELFKNAMRA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L255 | HMLFELFKNAM | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L306 | RITDRLFSYTY | 2 | Mus musculus, Rattus norvegicus | L306 | RIIDRLFSYTY | 1 | Homo sapiens | L334 | GFGYGLPISRL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L350 | QGDLNLYSMSG | 2 | Mus musculus, Rattus norvegicus | L350 | QGDLNLYSLSG | 1 | Homo sapiens | N258 | FELFKNAMRAT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | P335 | FGYGLPISRLY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R261 | FKNAMRATVEH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S312 | FSYTYSTAPTP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T313 | SYTYSTAPTPV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T358 | MSGYGTDAIIY | 2 | Mus musculus, Rattus norvegicus | T358 | LSGYGTDAIIY | 1 | Homo sapiens | V298 | DRGGGVPLRIT | 2 | Mus musculus, Rattus norvegicus | V298 | DRGGGVPLRII | 1 | Homo sapiens | Y311 | LFSYTYSTAPT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Y332 | LAGFGYGLPIS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus |
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