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 CDK1
Gene summary
Basic gene Info.Gene symbolCDK1
Gene namecyclin-dependent kinase 1
SynonymsCDC2|CDC28A|P34CDC2
CytomapUCSC genome browser: 10q21.1
Type of geneprotein-coding
RefGenesNM_001170406.1,
NM_001170407.1,NM_001786.4,NM_033379.4,NM_001130829.1,
Descriptioncell cycle controller CDC2cell division control protein 2 homologcell division cycle 2, G1 to S and G2 to Mcell division protein kinase 1p34 protein kinase
Modification date20141222
dbXrefs MIM : 116940
HGNC : HGNC
Ensembl : ENSG00000170312
HPRD : 00302
Vega : OTTHUMG00000018290
ProteinUniProt: P06493
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CDK1
BioGPS: 983
PathwayNCI Pathway Interaction Database: CDK1
KEGG: CDK1
REACTOME: CDK1
Pathway Commons: CDK1
ContextiHOP: CDK1
ligand binding site mutation search in PubMed: CDK1
UCL Cancer Institute: CDK1
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0018105peptidyl-serine phosphorylation11298763
GO:0018107peptidyl-threonine phosphorylation11298763
GO:0034501protein localization to kinetochore18195732
GO:0043066negative regulation of apoptotic process11069302


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Ligand binding site mutations for CDK1
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
L135I136NLUAD1
V18V18LLUSC1
L135L134FUCEC1
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 CDK1
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
L135I136N-1.6016167
L135L134F-0.98830569
V18V18L-0.42265621
(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 CDK1 from PDB

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Differential gene expression and gene-gene network for CDK1
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 CDK1 and the right PPI network was created from samples without mutations in the LBS of CDK1. 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 CDK1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0079744Lymphoma, Large B-Cell, Diffuse2Biomarker

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

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Pharmacological information for CDK1
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
ExperimentalDB02052Indirubin-3'-MonoximeSmall molecule
ExperimentalDB02116OlomoucineSmall molecule
ExperimentalDB02950HymenialdisineSmall molecule
ExperimentalDB03428SU9516Small molecule
Experimental|investigationalDB03496FlavopiridolSmall molecule
ExperimentalDB04014AlsterpaulloneSmall molecule
InvestigationalDB05037AT7519Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CDK1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
LZ9{[(2,6-DIFLUOROPHENYL)CARBONYL]AMINO}-N-(4-FLUOROPHENYL)-1H-PYRAZOLE-3-CARBOXAMIDE4y72AV18 L135


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Conservation information for LBS of CDK1
Multiple alignments for P06493 in multiple species
LBSAA sequence# speciesSpecies
A31TGQVVAMKKIR3Homo sapiens, Gallus gallus, Bos taurus
A31TGQIVAMKKIR3Drosophila melanogaster, Mus musculus, Rattus norvegicus
A31TNAMVAMKKIR1Caenorhabditis elegans
D146TIKLADFGLAR4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
D146AIKLADFGLAR1Caenorhabditis elegans
D146LIKVADFGLGR1Drosophila melanogaster
D146VIKLADFGLAR1Gallus gallus
D86EFLSMDLKKYL5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
D86EFLSFDLKRYM1Caenorhabditis elegans
D86EFLSMDLKKYM1Drosophila melanogaster
E81LYLIFEFLSMD5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
E81LFLIFEFLSFD1Caenorhabditis elegans
E81IYLIFEFLSMD1Drosophila melanogaster
F80RLYLIFEFLSM5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
F80RLFLIFEFLSF1Caenorhabditis elegans
F80RIYLIFEFLSM1Drosophila melanogaster
F82YLIFEFLSMDL6Homo sapiens, Drosophila melanogaster, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
F82FLIFEFLSFDL1Caenorhabditis elegans
I10TKIEKIGEGTY3Homo sapiens, Gallus gallus, Bos taurus
I10IKIEKIGEGTY2Mus musculus, Rattus norvegicus
I10TKLEKIGEGTY1Caenorhabditis elegans
I10EKIEKIGEGTY1Drosophila melanogaster
K33QVVAMKKIRLE3Homo sapiens, Gallus gallus, Bos taurus
K33QIVAMKKIRLE3Drosophila melanogaster, Mus musculus, Rattus norvegicus
K33AMVAMKKIRLE1Caenorhabditis elegans
K89SMDLKKYLDSI4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
K89SFDLKRYMDQL1Caenorhabditis elegans
K89SMDLKKYMDSL1Drosophila melanogaster
K89SMDLKKYLDTI1Gallus gallus
L135KPQNLLIDDKG5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
L135KPQNLLVDNNG1Caenorhabditis elegans
L135KPQNLLIDKSG1Drosophila melanogaster
L83LIFEFLSMDLK6Homo sapiens, Drosophila melanogaster, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
L83LIFEFLSFDLK1Caenorhabditis elegans
S84IFEFLSMDLKK6Homo sapiens, Drosophila melanogaster, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
S84IFEFLSFDLKR1Caenorhabditis elegans
V18GTYGVVYKGRH5Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus
V18GTYGVVYKGKN1Caenorhabditis elegans
V18GTYGVVYKGRN1Drosophila melanogaster
V64RHPNIVSLQDV4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
V64QHPNVVGLEAV1Caenorhabditis elegans
V64KHENIVCLEDV1Drosophila melanogaster
V64HHPNIVCLQDV1Gallus gallus
Y15IGEGTYGVVYK7Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus


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