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 XRCC5
Gene summary
Basic gene Info.Gene symbolXRCC5
Gene nameX-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)
CytomapUCSC genome browser: 2q35
Type of geneprotein-coding
Description86 kDa subunit of Ku antigenATP-dependent DNA helicase 2 subunit 2ATP-dependent DNA helicase II 80 kDa subunitCTC box-binding factor 85 kDa subunitCTC85CTCBFDNA repair protein XRCC5Ku autoantigen, 80kDaKu86 autoantigen related protein 1TLAAX-ray
Modification date20141207
dbXrefs MIM : 194364
Ensembl : ENSG00000079246
HPRD : 08935
Vega : OTTHUMG00000133059
ProteinUniProt: P13010
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_XRCC5
BioGPS: 7520
PathwayNCI Pathway Interaction Database: XRCC5
Pathway Commons: XRCC5
ContextiHOP: XRCC5
ligand binding site mutation search in PubMed: XRCC5
UCL Cancer Institute: XRCC5
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for XRCC5
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 XRCC5
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 XRCC5 from PDB

Differential gene expression and gene-gene network for XRCC5
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 XRCC5 and the right PPI network was created from samples without mutations in the LBS of XRCC5. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for XRCC5
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for XRCC5
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 XRCC5 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids1jeyBK7 L85 Y397
NUCNucleic Acids1jeyBW276

Conservation information for LBS of XRCC5
Multiple alignments for P13010 in multiple species
LBSAA sequence# speciesSpecies
A401YDK-RANPQVG1Homo sapiens
A401SKD-KGVPVLL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A401WRNGQGNVVVG1Arabidopsis thaliana
A401YDK-RSNPQVG1Mus musculus
D398VRYAYDK-RAN1Homo sapiens
D398ARFVSKD-KGV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D398VRCVWRNGQGN1Arabidopsis thaliana
D398VRYAYDK-RSN1Mus musculus
E53ENK-DEIALVL1Homo sapiens
E53NRKTDVVGIVG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E53NKY-DEVGIVV1Arabidopsis thaliana
E53ESK-DEIALVL1Mus musculus
K125HETIGKKFEKR1Homo sapiens
K125RHCKKNKWKKK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K125KMYGNAHKGKK1Arabidopsis thaliana
K125RETIGKKFGKK1Mus musculus
K126ETIGKKFEKRH1Homo sapiens
K126HCKKNKWKKKM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K126MYGNAHKGKKR1Arabidopsis thaliana
K126ETIGKKFGKKH1Mus musculus
K265RIAAYKSILQE1Homo sapiens
K265QVERYPRTRLT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K265KVWVYKKVAEE1Arabidopsis thaliana
K265KIVAYKSIVQE1Mus musculus
K325IVPFSKVDEEQ1Homo sapiens
K325IVPISRSDEDV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K325VIPISPDQIET1Arabidopsis thaliana
K325IIPFSKVDEEQ1Mus musculus
K338YKSEGKCFSVL2Homo sapiens, Mus musculus
K338LDTI-PGYEIL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K338FKTD-KGMKLL1Arabidopsis thaliana
K399RYAYDK-RANP1Homo sapiens
K399RFVSKD-KGVP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K399RCVWRNGQGNV1Arabidopsis thaliana
K399RYAYDK-RSNP1Mus musculus
K7VRSGNKAAVVL1Homo sapiens
K7--MSDKECTVF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K7-MARNREGLVL1Arabidopsis thaliana
K7AWSGNKAAVVL1Mus musculus
L85HRHLMLPDFDL1Homo sapiens
L85LYPIQTALFSK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L85LRNIRV--VDE1Arabidopsis thaliana
L85CRHLMLPDFDL1Mus musculus
N402DK-RANPQVGV1Homo sapiens
N402KD-KGVPVLLV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N402RNGQGNVVVGV1Arabidopsis thaliana
N402DK-RSNPQVGV1Mus musculus
R242FKKIERHSIH-1Homo sapiens
R242-KPWVRKVRPV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R242LK--TRRVAPV1Arabidopsis thaliana
R242FKKIERRSMP-1Mus musculus
R400AYDK-RANPQV1Homo sapiens
R400VSKD-KGVPVL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R400VWRNGQGNVVV1Arabidopsis thaliana
R400AYDK-RSNPQV1Mus musculus
R431FMEDLRQYMFS2Homo sapiens, Mus musculus
R431FAEDVRPYSFS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R431FAEDVREFPFP1Arabidopsis thaliana
R486KIPNPRFQRLF1Homo sapiens
R486NTFSMIPHRLQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R486LTPNPVLQRFY1Arabidopsis thaliana
R486KIPNPEFQRLY1Mus musculus
T275ERVKKTWTVVD1Homo sapiens
T275TKPPTSSAFYE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T275ERLPTLKMYSD1Arabidopsis thaliana
T275EKFKKSWVVVD1Mus musculus
W276RVKKTWTVVD-1Homo sapiens
W276KPPTSSAFYEN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
W276RLPTLKMYSDK1Arabidopsis thaliana
W276KFKKSWVVVD-1Mus musculus
Y397IVRYAYDK-RA1Homo sapiens
Y397LARFVSKD-KG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y397IVRCVWRNGQG1Arabidopsis thaliana
Y397IVRYAYDK-RS1Mus musculus

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