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 CDK7
Gene summary
Basic gene Info.Gene symbolCDK7
Gene namecyclin-dependent kinase 7
CytomapUCSC genome browser: 5q12.1
Type of geneprotein-coding
Description39 KDa protein kinaseCAKCDK-activating kinase 1TFIIH basal transcription factor complex kinase subunitcell division protein kinase 7cyclin-dependent kinase 7 (MO15 homolog, Xenopus laevis, cdk-activating kinase)homolog of Xenopus MO15 Cdk-activating
Modification date20141207
dbXrefs MIM : 601955
Ensembl : ENSG00000134058
HPRD : 15993
Vega : OTTHUMG00000099358
ProteinUniProt: P50613
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CDK7
BioGPS: 1022
PathwayNCI Pathway Interaction Database: CDK7
Pathway Commons: CDK7
ContextiHOP: CDK7
ligand binding site mutation search in PubMed: CDK7
UCL Cancer Institute: CDK7
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006200ATP catabolic process9852112
GO:0006366transcription from RNA polymerase II promoter9852112
GO:0045944positive regulation of transcription from RNA polymerase II promoter8692841

Ligand binding site mutations for CDK7
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 CDK7
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 CDK7 from PDB

Differential gene expression and gene-gene network for CDK7
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 CDK7 and the right PPI network was created from samples without mutations in the LBS of CDK7. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for CDK7
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0031117Peripheral Nervous System Diseases1Biomarker

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

Pharmacological information for CDK7
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
ExperimentalDB02482PhosphonothreonineSmall molecule
Experimental|investigationalDB03496FlavopiridolSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CDK7 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ATPATP1ua2DV26 A39 D92
ATPATP1ua2AV26 A39 D92 S161
ATPATP1ua2BV26 A39 D92 S161
ATPATP1ua2CV26 A39 S161

Conservation information for LBS of CDK7
Multiple alignments for P50613 in multiple species
LBSAA sequence# speciesSpecies
A24GEGQFATVYKA2Homo sapiens, Mus musculus
A24GEGTYGVVYKA1Arabidopsis thaliana
A24GEGQFANVYLA1Caenorhabditis elegans
A24GEGTYAVVYLG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A24GEGTYAVVFLG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A39TNQIVAIKKIK2Homo sapiens, Mus musculus
A39TGKTVAVKKIR1Arabidopsis thaliana
A39SGECVAIKKIK1Caenorhabditis elegans
A39TGRKIAIKEIK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A39TNRRVAIKKIK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D92ISLVFDFMETD2Homo sapiens, Mus musculus
D92LHLVFEYMQTD1Arabidopsis thaliana
D92IQLVFDFMDTD1Caenorhabditis elegans
D92LNLVLEFLPTD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D92LNIILEFLDSD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E20LDFLGEGQFAT2Homo sapiens, Mus musculus
E20RQILGEGTYGV1Arabidopsis thaliana
E20IKHLGEGQFAN1Caenorhabditis elegans
E20EKKVGEGTYAV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E20ERKVGEGTYAV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F23LGEGQFATVYK2Homo sapiens, Mus musculus
F23LGEGTYGVVYK1Arabidopsis thaliana
F23LGEGQFANVYL1Caenorhabditis elegans
F23VGEGTYAVVYL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F23VGEGTYAVVFL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F93SLVFDFMETDL2Homo sapiens, Mus musculus
F93HLVFEYMQTDL1Arabidopsis thaliana
F93QLVFDFMDTDL1Caenorhabditis elegans
F93NLVLEFLPTDL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F93NIILEFLDSDL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G21DFLGEGQFATV2Homo sapiens, Mus musculus
G21QILGEGTYGVV1Arabidopsis thaliana
G21KHLGEGQFANV1Caenorhabditis elegans
G21KKVGEGTYAVV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G21RKVGEGTYAVV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I75SHPNIIGLLDA2Homo sapiens, Mus musculus
I75NHPHIVELIDA1Arabidopsis thaliana
I75HHDNIIGLRDV1Caenorhabditis elegans
I75QHPNVIELIDI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I75RHDNVIELVDV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L18EKLDFLGEGQF2Homo sapiens, Mus musculus
L18LRRQILGEGTY1Arabidopsis thaliana
L18DTIKHLGEGQF1Caenorhabditis elegans
L18TKEKKVGEGTY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L18VKERKVGEGTY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M94LVFDFMETDLE2Homo sapiens, Mus musculus
M94LVFEYMQTDLE1Arabidopsis thaliana
M94LVFDFMDTDLE1Caenorhabditis elegans
M94LVLEFLPTDLE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M94IILEFLDSDLE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N141RDLKPNNLLLD2Homo sapiens, Mus musculus
N141RDMKPNNLLIG1Arabidopsis thaliana
N141RDLKPNNLLMN1Caenorhabditis elegans
N141RDLKPNNLLFS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N141RDLKPNNLLIS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N142DLKPNNLLLDE2Homo sapiens, Mus musculus
N142DMKPNNLLIGE1Arabidopsis thaliana
N142DLKPNNLLMNK1Caenorhabditis elegans
N142DLKPNNLLFSP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N142DLKPNNLLISS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q22FLGEGQFATVY2Homo sapiens, Mus musculus
Q22ILGEGTYGVVY1Arabidopsis thaliana
Q22HLGEGQFANVY1Caenorhabditis elegans
Q22KVGEGTYAVVY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q22KVGEGTYAVVF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S161FGLAKSFGSPN2Homo sapiens, Mus musculus
S161FGLARLFGSPN1Arabidopsis thaliana
S161FGLARFFGSPN1Caenorhabditis elegans
S161FGLARAIPAPH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S161FGLSRDFGTPS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V26GQFATVYKARD2Homo sapiens, Mus musculus
V26GTYGVVYKATD1Arabidopsis thaliana
V26GQFANVYLAQD1Caenorhabditis elegans
V26GTYAVVYLGCQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V26GTYAVVFLGRQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)

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