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 TDP1
Gene summary
Basic gene Info.Gene symbolTDP1
Gene nametyrosyl-DNA phosphodiesterase 1
Synonyms-
CytomapUCSC genome browser: 14q32.11
Type of geneprotein-coding
RefGenesNM_001008744.1,
NM_018319.3,
Descriptiontyr-DNA phosphodiesterase 1
Modification date20141219
dbXrefs MIM : 607198
HGNC : HGNC
Ensembl : ENSG00000042088
HPRD : 06226
Vega : OTTHUMG00000171016
ProteinUniProt: Q9NUW8
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TDP1
BioGPS: 55775
PathwayNCI Pathway Interaction Database: TDP1
KEGG: TDP1
REACTOME: TDP1
Pathway Commons: TDP1
ContextiHOP: TDP1
ligand binding site mutation search in PubMed: TDP1
UCL Cancer Institute: TDP1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0000012single strand break repair15811850
GO:0006281DNA repair17948061
GO:0006302double-strand break repair12023295


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Ligand binding site mutations for TDP1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
D230D230NKIRC1
A258A258VPRAD1
W590I589RSKCM1
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 TDP1
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
W590I589R-1.5660599
A258A258V-1.2447056
D230D230N-1.1164753
(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 TDP1 from PDB

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Differential gene expression and gene-gene network for TDP1
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 TDP1 and the right PPI network was created from samples without mutations in the LBS of TDP1. 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 TDP1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1846574Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy1Biomarker, GeneticVariation

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

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Pharmacological information for TDP1
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of TDP1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids1nopAA258 W590
IIIPeptide ligand (LYS,LEU,ASN,TYR,TYR,ASP)1rffBD230
IIIPeptide ligand (LYS,LEU,ASN,TYR,LEU)1nopAD230 W590
IIIPeptide ligand (LYS,LEU,ASN,TYR,TYR,ASP)1rffAD230 W590
IIIPeptide ligand (LYS,LEU,ASN,TYR,LYS)1rfiAD230 W590
NUCNucleic Acids1nopBW590
NUCNucleic Acids1rffAW590
NUCNucleic Acids1rffBW590
NUCNucleic Acids1rfiAW590
IIIPeptide ligand (LEU,ASN,TYR)1rfiBW590
NUCNucleic Acids1rg1BW590
NUCNucleic Acids1rg2AW590
OTS(S)-OCTOPAMINE1rg2AW590
NUCNucleic Acids1rg2BW590
OTS(S)-OCTOPAMINE1rg2BW590
OTS(S)-OCTOPAMINE1rgtBW590
NUCNucleic Acids1rguAW590
NUCNucleic Acids1rguBW590
NUCNucleic Acids1rh0BW590


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Conservation information for LBS of TDP1
Multiple alignments for Q9NUW8 in multiple species
LBSAA sequence# speciesSpecies
A258AKLDIAFGTHH2Homo sapiens, Rattus norvegicus
A258VKMPTPFATSH1Drosophila melanogaster
A258PRLPISFGTHH1Arabidopsis thaliana
A258ASLPIPFGTHH1Caenorhabditis elegans
A520ANLSKAAWGAL2Homo sapiens, Rattus norvegicus
A520ANLSKAAWGCF1Drosophila melanogaster
A520SNLSKAAWGAL1Arabidopsis thaliana
A520ANLSKAAWGEV1Caenorhabditis elegans
C205AQFNYCFDVDW1Homo sapiens
C205VQINFMVDIGW1Drosophila melanogaster
C205ILSNYMVDIDW1Arabidopsis thaliana
C205LHFSFMLDFEF1Caenorhabditis elegans
C205AQFNYCFDVNW1Rattus norvegicus
D207FNYCFDVDWLV1Homo sapiens
D207INFMVDIGWLL1Drosophila melanogaster
D207SNYMVDIDWLM1Arabidopsis thaliana
D207FSFMLDFEFLI1Caenorhabditis elegans
D207FNYCFDVNWLI1Rattus norvegicus
D230LLVHGDKREAK2Homo sapiens, Rattus norvegicus
D230LLLYGD---ES1Drosophila melanogaster
D230MVIHGEG-DGR1Arabidopsis thaliana
D230TLVVGA--PDA1Caenorhabditis elegans
F206QFNYCFDVDWL1Homo sapiens
F206QINFMVDIGWL1Drosophila melanogaster
F206LSNYMVDIDWL1Arabidopsis thaliana
F206HFSFMLDFEFL1Caenorhabditis elegans
F206QFNYCFDVNWL1Rattus norvegicus
F259KLDIAFGTHHT2Homo sapiens, Rattus norvegicus
F259KMPTPFATSHT1Drosophila melanogaster
F259RLPISFGTHHS1Arabidopsis thaliana
F259SLPIPFGTHHT1Caenorhabditis elegans
G402QFSSVGSLGAD1Homo sapiens
G402QSSSIGSLGAN1Drosophila melanogaster
G402QFSSLGSL---1Arabidopsis thaliana
G402QCSSIGSLGSA1Caenorhabditis elegans
G402QFSSIGSLGPD1Rattus norvegicus
G458GYPAGGSLPYS1Homo sapiens
G458GMLGGGCLPYG1Drosophila melanogaster
G458GYAAGNAIPSP1Arabidopsis thaliana
G458GYAGGCSVPYR1Caenorhabditis elegans
G458GYPAGGSLPYG1Rattus norvegicus
H237REAKAHLHAQA1Homo sapiens
H237--ESPELLSIG1Drosophila melanogaster
H237-DGRQEYIQRK1Arabidopsis thaliana
H237-PDAPDLLKCT1Caenorhabditis elegans
H237REAKADLHAQA1Rattus norvegicus
H263AFGTHHTKMML2Homo sapiens, Rattus norvegicus
H263PFATSHTKMMF1Drosophila melanogaster
H263SFGTHHSKAIF1Arabidopsis thaliana
H263PFGTHHTKMSI1Caenorhabditis elegans
H493SNAMPHIKTYM2Homo sapiens, Rattus norvegicus
H493SRAMPHIKSYT1Drosophila melanogaster
H493GRAMPHIKTFT1Arabidopsis thaliana
H493TNAVPHCKTYV1Caenorhabditis elegans
I285HTSNLIHADWH1Homo sapiens
I285STANLYEDDWH1Drosophila melanogaster
I285HTANLIHVDWN1Arabidopsis thaliana
I285STANLVPDDWE1Caenorhabditis elegans
I285HTSNLIREDWH1Rattus norvegicus
K265GTHHTKMMLLL2Homo sapiens, Rattus norvegicus
K265ATSHTKMMFLG1Drosophila melanogaster
K265GTHHSKAIFLV1Arabidopsis thaliana
K265GTHHTKMSILE1Caenorhabditis elegans
K469IQTAEKQNWLH1Homo sapiens
K469KNTNDKQPWLK1Drosophila melanogaster
K469LKNVEK-PFLK1Arabidopsis thaliana
K469NSVHARQKWLQ1Caenorhabditis elegans
K469IQTAEKQRWLH1Rattus norvegicus
K495AMPHIKTYMRP2Homo sapiens, Rattus norvegicus
K495AMPHIKSYTRF1Drosophila melanogaster
K495AMPHIKTFTRY1Arabidopsis thaliana
K495AVPHCKTYVKY1Caenorhabditis elegans
K519SANLSKAAWGA2Homo sapiens, Rattus norvegicus
K519SANLSKAAWGC1Drosophila melanogaster
K519SSNLSKAAWGA1Arabidopsis thaliana
K519SANLSKAAWGE1Caenorhabditis elegans
N283VIHTSNLIHAD1Homo sapiens
N283VISTANLYEDD1Drosophila melanogaster
N283VVHTANLIHVD1Arabidopsis thaliana
N283IVSTANLVPDD1Caenorhabditis elegans
N283VIHTSNLIRED1Rattus norvegicus
N516LVTSANLSKAA2Homo sapiens, Rattus norvegicus
N516VLTSANLSKAA1Drosophila melanogaster
N516LLTSSNLSKAA1Arabidopsis thaliana
N516LLTSANLSKAA1Caenorhabditis elegans
P461AGGSLPYSIQT1Homo sapiens
P461GGGCLPYGKNT1Drosophila melanogaster
P461AGNAIPSPLKN1Arabidopsis thaliana
P461GGCSVPYRNSV1Caenorhabditis elegans
P461AGGSLPYGIQT1Rattus norvegicus
Q241AHLHAQAKPYE1Homo sapiens
Q241PELLSIGKFKQ1Drosophila melanogaster
Q241QEYIQRKKP-A1Arabidopsis thaliana
Q241PDLLKCTKNQK1Caenorhabditis elegans
Q241ADLHAQAKPYA1Rattus norvegicus
R535--LMIRSYELG3Homo sapiens, Arabidopsis thaliana, Rattus norvegicus
R535PCLRIANYEAG1Drosophila melanogaster
R535--LMIRSWEMG1Caenorhabditis elegans
S400VGQFSSVGSLG1Homo sapiens
S400VCQSSSIGSLG1Drosophila melanogaster
S400IYQFSSLGSL-1Arabidopsis thaliana
S400VAQCSSIGSLG1Caenorhabditis elegans
S400VGQFSSIGSLG1Rattus norvegicus
S403FSSVGSLGADE1Homo sapiens
S403SSSIGSLGANV1Drosophila melanogaster
S403FSSLGSL---D1Arabidopsis thaliana
S403CSSIGSLGSAP1Caenorhabditis elegans
S403FSSIGSLGPDE1Rattus norvegicus
S459YPAGGSLPYSI1Homo sapiens
S459MLGGGCLPYGK1Drosophila melanogaster
S459YAAGNAIPSPL1Arabidopsis thaliana
S459YAGGCSVPYRN1Caenorhabditis elegans
S459YPAGGSLPYGI1Rattus norvegicus
S518TSANLSKAAWG4Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Rattus norvegicus
S518TSSNLSKAAWG1Arabidopsis thaliana
T261DIAFGTHHTKM2Homo sapiens, Rattus norvegicus
T261PTPFATSHTKM1Drosophila melanogaster
T261PISFGTHHSKA1Arabidopsis thaliana
T261PIPFGTHHTKM1Caenorhabditis elegans
W590DRPWIWNIPYV2Homo sapiens, Rattus norvegicus
W590DKPFLMD----1Drosophila melanogaster
W590DVPWSWDRGYS1Arabidopsis thaliana
W590DEPFVTDKKHE1Caenorhabditis elegans
Y204SAQFNYCFDVD1Homo sapiens
Y204TVQINFMVDIG1Drosophila melanogaster
Y204AILSNYMVDID1Arabidopsis thaliana
Y204SLHFSFMLDFE1Caenorhabditis elegans
Y204SAQFNYCFDVN1Rattus norvegicus


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