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 DDB1
Gene summary
Basic gene Info.Gene symbolDDB1
Gene namedamage-specific DNA binding protein 1, 127kDa
SynonymsDDBA|UV-DDB1|XAP1|XPCE|XPE|XPE-BF
CytomapUCSC genome browser: 11q12-q13
Type of geneprotein-coding
RefGenesNM_001923.4,
DescriptionDDB p127 subunitDNA damage-binding protein 1DNA damage-binding protein aHBV X-associated protein 1UV-DDB 1UV-damaged DNA-binding factorUV-damaged DNA-binding protein 1XAP-1XPE-binding factorxeroderma pigmentosum group E-complementing protein
Modification date20141222
dbXrefs MIM : 600045
HGNC : HGNC
Ensembl : ENSG00000167986
HPRD : 10952
Vega : OTTHUMG00000168209
ProteinUniProt: Q16531
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DDB1
BioGPS: 1642
PathwayNCI Pathway Interaction Database: DDB1
KEGG: DDB1
REACTOME: DDB1
Pathway Commons: DDB1
ContextiHOP: DDB1
ligand binding site mutation search in PubMed: DDB1
UCL Cancer Institute: DDB1
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:0035518histone H2A monoubiquitination22334663
GO:0042787protein ubiquitination involved in ubiquitin-dependent protein catabolic process11673459
GO:0070914UV-damage excision repair22334663


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Ligand binding site mutations for DDB1
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
R722P721LCOAD2
M910N908HBRCA1
F1003E1002KCOAD1
R722P721QCOAD1
R327R327CHNSC1
A381G380WKIRC1
A834G832SLUAD1
R722P721LOV1
R327R327CSKCM1
Y871V870AUCEC1
F1003E1002KUCEC1
V1033G1035SUCEC1
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 DDB1
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
F1003E1002K-1.4665512
Y871V870A-1.2741801
R722P721Q-1.1555262
V1033G1035S-0.89280716
R327R327C-0.81828746
M910N908H-0.56539781
R722P721L-0.48841342
A834G832S-0.48102932
A381G380W-0.13062324
(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 DDB1 from PDB
PDB IDPDB titlePDB structure
2B5MCrystal Structure of DDB1

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Differential gene expression and gene-gene network for DDB1
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 DDB1 and the right PPI network was created from samples without mutations in the LBS of DDB1. 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 DDB1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0242656Disease Progression1Biomarker
umls:C0038356Stomach Neoplasms1Biomarker

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

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Pharmacological information for DDB1
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 DDB1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (SER,LEU,VAL,TYR,TYR,LEU,LYS,ASN,ARG,GLU,VAL,ARG,LEU)3i7pAR327 A381 R722 M910 V1033
IIIPeptide ligand (ILE,LEU,PRO,LYS,VAL,LEU,HIS,LYS,ARG,THR,LEU,GLY,LEU,SER)3i7hAR327 A381 R722 Y871 F1003 V1033
IIIPeptide ligand (ASN,PHE,VAL,SER,TRP,HIS,ALA,ASN,ARG,GLN,LEU,GLY,MET,PRO)3i7kAR327 A381 R722 Y871 V1033
IIIPeptide ligand (HIS,LEU,LEU,TRP,ASP,VAL,ARG,LYS,ARG,SER,LEU,GLY,LEU)3i7oAR327 R722 A834 Y871 M910 V1033
IIIPeptide ligand (ASN,ALA,SER,SER,MET,LEU,ARG,LYS,SER,GLN,LEU,GLY,PHE)3i8cAR327 R722 Y871 F1003 V1033
IIIPeptide ligand (GLN,ALA,LEU,PRO,ALA,LEU,ARG,GLU,ARG,GLU,LEU,GLY,SER)3i8eAR327 R722 Y871 F1003 V1033
IIIPeptide ligand (ASN,ILE,THR,ARG,ASP,LEU,ILE,ARG,ARG,GLN,ILE,LYS,GLU)3i7nAR327 R722 Y871 M910 F1003 V1033
IIIPeptide ligand (GLN,ALA,LEU,PRO,ALA,LEU,ARG,GLU,ARG,GLU,LEU,GLY,SER)3i8eBR327 R722 Y871 M910 F1003 V1033
IIIPeptide ligand (SER,ILE,VAL,ARG,THR,LEU,HIS,GLN,HIS,LYS,LEU,GLY,ARG,ALA)3i7lAR327 R722 Y871 M910 V1033
IIIPeptide ligand (SER,VAL,VAL,GLY,PHE,LEU,SER,GLN,ARG,GLY,LEU,HIS,GLY)3i89AR327 Y871 M910 F1003 V1033


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Conservation information for LBS of DDB1
Multiple alignments for Q16531 in multiple species
LBSAA sequence# speciesSpecies
A381VTCSGAFKEGS4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
A381VTCSGAFKDGS1Arabidopsis thaliana
A381VTCSGAYKDGS1Arabidopsis thaliana
A381ITCSGSFKDGS1Drosophila melanogaster
A834FIVGTAMVYPE4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
A834YCVGTAYVLPE2Arabidopsis thaliana, Arabidopsis thaliana
A834YVVATSLVIPE1Drosophila melanogaster
A841VYPEEAEPKQG4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
A841VLPEENEPTKG2Arabidopsis thaliana, Arabidopsis thaliana
A841VIPEEPEPKVG1Drosophila melanogaster
E787FGEEVEVHNLL4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
E787NSEESEMHFVR1Arabidopsis thaliana
E787SAEESESHFVR1Arabidopsis thaliana
E787VGQEIDVHNLL1Drosophila melanogaster
E839AMVYPEEAEPK4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
E839AYVLPEENEPT2Arabidopsis thaliana, Arabidopsis thaliana
E839SLVIPEEPEPK1Drosophila melanogaster
E840MVYPEEAEPKQ4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
E840YVLPEENEPTK2Arabidopsis thaliana, Arabidopsis thaliana
E840LVIPEEPEPKV1Drosophila melanogaster
F1003FHLGEFVNVFC3Homo sapiens, Mus musculus, Bos taurus
F1003YHLGEFVNRFR1Arabidopsis thaliana
F1003YHIGEFVNRFR1Arabidopsis thaliana
F1003FHLGDTVNVFR1Drosophila melanogaster
F1003SHLGEFVNVFC1Gallus gallus
F382TCSGAFKEGSL4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
F382TCSGAFKDGSL1Arabidopsis thaliana
F382TCSGAYKDGSL1Arabidopsis thaliana
F382TCSGSFKDGSL1Drosophila melanogaster
H789EEVEVHNLLII4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
H789EESEMHFVRLL1Arabidopsis thaliana
H789EESESHFVRLL1Arabidopsis thaliana
H789QEIDVHNLLVI1Drosophila melanogaster
L328FVGSRLGDSQL4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
L328FVGSSYGDSQL2Arabidopsis thaliana, Arabidopsis thaliana
L328YIGARHGDSQL1Drosophila melanogaster
L814QNEYALSLVSC4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
L814SFEYGCSILSC1Arabidopsis thaliana
L814AFECGCSILSC1Arabidopsis thaliana
L814APETISSLMSA1Drosophila melanogaster
L912NNIMALYLKTK4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
L912GHILALYVQTR2Arabidopsis thaliana, Arabidopsis thaliana
L912NMIAALFLKAK1Drosophila melanogaster
M910HYNNIMALYLK4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
M910HHGHILALYVQ2Arabidopsis thaliana, Arabidopsis thaliana
M910IQNMIAALFLK1Drosophila melanogaster
M954FNPNWMSAVEI4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
M954YNANWMSAVEI1Arabidopsis thaliana
M954YNANWMTAVEI1Arabidopsis thaliana
M954CEPKWMRAVEI1Drosophila melanogaster
N1005LGEFVNVFCHG4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
N1005LGEFVNRFRHG1Arabidopsis thaliana
N1005IGEFVNRFRHG1Arabidopsis thaliana
N1005LGDTVNVFRHG1Drosophila melanogaster
N970FLGAENAFNLF4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
N970YLGAENNFNLL1Arabidopsis thaliana
N970YLGTDNCFNIF1Arabidopsis thaliana
N970FLGSETNGNLF1Drosophila melanogaster
P358FTNLGPIVDMC4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
P358YINLGPIVDFC1Arabidopsis thaliana
P358YVNLGPIVDFC1Arabidopsis thaliana
P358FTNLAPILDIA1Drosophila melanogaster
P838TAMVYPEEAEP4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
P838TAYVLPEENEP2Arabidopsis thaliana, Arabidopsis thaliana
P838TSLVIPEEPEP1Drosophila melanogaster
P843PEEAEPKQGRI4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
P843PEENEPTKGRI2Arabidopsis thaliana, Arabidopsis thaliana
P843PEEPEPKVGRI1Drosophila melanogaster
R327VFVGSRLGDSQ4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
R327VFVGSSYGDSQ2Arabidopsis thaliana, Arabidopsis thaliana
R327LYIGARHGDSQ1Drosophila melanogaster
R722LYESPRKICYQ4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
R722LGEHARRICHQ1Arabidopsis thaliana
R722IGEHARRICHQ1Arabidopsis thaliana
R722LGEGPRRIAYQ1Drosophila melanogaster
S955NPNWMSAVEIL4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
S955NANWMSAVEIL1Arabidopsis thaliana
S955NANWMTAVEIL1Arabidopsis thaliana
S955EPKWMRAVEIL1Drosophila melanogaster
V1033VLFGTVNGMIG4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
V1033VIFGTVNGVIG1Arabidopsis thaliana
V1033VIFGTVSGMIG1Arabidopsis thaliana
V1033VLYGTCNGAIG1Drosophila melanogaster
V360NLGPIVDMCVV4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
V360NLGPIVDFCVV2Arabidopsis thaliana, Arabidopsis thaliana
V360NLAPILDIAVV1Drosophila melanogaster
V836VGTAMVYPEEA4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
V836VGTAYVLPEEN2Arabidopsis thaliana, Arabidopsis thaliana
V836VATSLVIPEEP1Drosophila melanogaster
W953DFNPNWMSAVE4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
W953DYNANWMSAVE1Arabidopsis thaliana
W953DYNANWMTAVE1Arabidopsis thaliana
W953DCEPKWMRAVE1Drosophila melanogaster
Y812FLQNEYALSLV4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
Y812LDSFEYGCSIL1Arabidopsis thaliana
Y812LDAFECGCSIL1Arabidopsis thaliana
Y812FVAPETISSLM1Drosophila melanogaster
Y837GTAMVYPEEAE4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
Y837GTAYVLPEENE2Arabidopsis thaliana, Arabidopsis thaliana
Y837ATSLVIPEEPE1Drosophila melanogaster
Y871VKGAVYSMVEF4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
Y871TKGAVYSLNAF2Arabidopsis thaliana, Arabidopsis thaliana
Y871VDGTCYALVEF1Drosophila melanogaster
Y913NIMALYLKTKG4Homo sapiens, Gallus gallus, Mus musculus, Bos taurus
Y913HILALYVQTRG2Arabidopsis thaliana, Arabidopsis thaliana
Y913MIAALFLKAKG1Drosophila melanogaster


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