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 DDB2
Gene summary
Basic gene Info.Gene symbolDDB2
Gene namedamage-specific DNA binding protein 2, 48kDa
CytomapUCSC genome browser: 11p12-p11
Type of geneprotein-coding
DescriptionDDB p48 subunitDNA damage-binding protein 2UV-DDB 2UV-damaged DNA-binding protein 2damage-specific DNA-binding protein 2xeroderma pigmentosum group E protein
Modification date20141222
dbXrefs MIM : 600811
Ensembl : ENSG00000134574
HPRD : 02886
Vega : OTTHUMG00000187453
ProteinUniProt: Q92466
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DDB2
BioGPS: 1643
PathwayNCI Pathway Interaction Database: DDB2
Pathway Commons: DDB2
ContextiHOP: DDB2
ligand binding site mutation search in PubMed: DDB2
UCL Cancer Institute: DDB2
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0000209protein polyubiquitination12732143
GO:0009411response to UV12732143
GO:0035518histone H2A monoubiquitination22334663
GO:0051865protein autoubiquitination12732143
GO:0070914UV-damage excision repair22334663

Ligand binding site mutations for DDB2
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.

Clinical information for DDB2 from My Cancer Genome.
Damage-specific DNA binding protein 2, 47kDa (DDB2) is a gene that encodes a protein that functions in repair of UV light damaged DNA. Missense mutations, silent mutations, frameshift deletions, and nonsense mutations are observed in cancers such as endometrial cancer, urinary tract cancer, and cervical cancer. Modified: August 27, 2015

Protein structure related information for DDB2
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 DDB2 from PDB
PDB IDPDB titlePDB structure
3EI4Structure of the hsDDB1-hsDDB2 complex

Differential gene expression and gene-gene network for DDB2
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 DDB2 and the right PPI network was created from samples without mutations in the LBS of DDB2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for DDB2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1848411Xeroderma Pigmentosum, Complementation Group E4Biomarker, GeneticVariation

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

Pharmacological information for DDB2
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 DDB2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids4e54BH333 H336
NUCNucleic Acids4e5zBI394
NUCNucleic Acids4e5zBP290 H333 H336
NUCNucleic Acids4e54BR370

Conservation information for LBS of DDB2
Multiple alignments for Q92466 in multiple species
LBSAA sequence# speciesSpecies
A155IKGIGAGGSIT2Homo sapiens, Bos taurus
A155--GNIHSVQVN1Arabidopsis thaliana
A155LKGIGAGGSIT1Mus musculus
A155IKGKGPGDSLG1Gallus gallus
A155IPGIGAGGCIT1Xenopus tropicalis
F334HPHRHFQHLTP3Homo sapiens, Mus musculus, Bos taurus
F334HSNDFNRHLTP1Arabidopsis thaliana
F334HPHRQFQHLTP1Gallus gallus
F334HPHRQFQHLTA1Xenopus tropicalis
G156KGIGAGGSITG3Homo sapiens, Mus musculus, Bos taurus
G156-GNIHSVQVNN1Arabidopsis thaliana
G156KGKGPGDSLGD1Gallus gallus
G156PGIGAGGCITG1Xenopus tropicalis
G393DPESSGISSLN1Homo sapiens
G393DPNITTITPVN1Arabidopsis thaliana
G393DPGYSGITSLN1Mus musculus
G393DPESSGIMSLN1Bos taurus
G393DPNASGIISLN1Gallus gallus
G393DPYASGIVSLN1Xenopus tropicalis
G412LASGMGFNILI2Gallus gallus, Xenopus tropicalis
G412LASAMGYHILI1Homo sapiens
G412LASGSSRSLFI1Arabidopsis thaliana
G412LASTMGYHILI1Mus musculus
G412LASVMGYHILV1Bos taurus
H333PHPHRHFQHLT2Homo sapiens, Bos taurus
H333PHPHRQFQHLT2Gallus gallus, Xenopus tropicalis
H333VHSNDFNRHLT1Arabidopsis thaliana
H333SHPHRHFQHLT1Mus musculus
H336HRHFQHLTPIK3Homo sapiens, Mus musculus, Bos taurus
H336NDFNRHLTPFK1Arabidopsis thaliana
H336HRQFQHLTPIK1Gallus gallus
H336HRQFQHLTAIK1Xenopus tropicalis
I394PESSGISSLNE1Homo sapiens
I394PNITTITPVNK1Arabidopsis thaliana
I394PGYSGITSLNE1Mus musculus
I394PESSGIMSLNE1Bos taurus
I394PNASGIISLNK1Gallus gallus
I394PYASGIVSLNK1Xenopus tropicalis
K132VAVGSKGGDII2Gallus gallus, Xenopus tropicalis
K132VAVGSKGGDIM1Homo sapiens
K132LLSGDKKGQIG1Arabidopsis thaliana
K132LAVGSKGGDIM1Mus musculus
K132LAVGSKGGDIL1Bos taurus
K242NLRMHKKKVTH2Homo sapiens, Bos taurus
K242-IHKQGSKVCG1Arabidopsis thaliana
K242NLRMHKKKVAH1Mus musculus
K242KLKLHKKKVTH1Gallus gallus
K242KLRLHKKKVTH1Xenopus tropicalis
K243LRMHKKKVTHV2Homo sapiens, Bos taurus
K243IHKQGSKVCGL1Arabidopsis thaliana
K243LRMHKKKVAHV1Mus musculus
K243LKLHKKKVTHV1Gallus gallus
K243LRLHKKKVTHV1Xenopus tropicalis
K244RMHKKKVTHVA2Homo sapiens, Bos taurus
K244HKQGSKVCGLD1Arabidopsis thaliana
K244RMHKKKVAHVA1Mus musculus
K244KLHKKKVTHVE1Gallus gallus
K244RLHKKKVTHVE1Xenopus tropicalis
M177FYASSMEGTTR1Homo sapiens
M177VYSASSDGTIG1Arabidopsis thaliana
M177FFASSMEGTTR1Mus musculus
M177FFTSSMEGTTR1Bos taurus
M177LYVASGDGTLS1Gallus gallus
M177LYTSSVAGSTV1Xenopus tropicalis
N201-----NIWFCS1Homo sapiens
N201GANSWKMLY-G1Arabidopsis thaliana
N201-----KVWFCS1Mus musculus
N201-----NVWFCS1Bos taurus
N201ENHNVCCWYCS1Gallus gallus
N201----WAMWYCS1Xenopus tropicalis
P290LPHRHPVNAAC2Homo sapiens, Mus musculus
P290LAHKRVVNSAY1Arabidopsis thaliana
P290LPHRHPVNAAH1Bos taurus
P290LPHDKPVNAAY1Gallus gallus
P290LPHARGVNSAY1Xenopus tropicalis
Q308LLTTDQKSEIR2Homo sapiens, Bos taurus
Q308ILTTCQDNRIR1Arabidopsis thaliana
Q308LLTTDQNNEIR1Mus musculus
Q308LLSTDQRNEIR1Gallus gallus
Q308LLTTDQHSEIR1Xenopus tropicalis
Q335PHRHFQHLTPI3Homo sapiens, Mus musculus, Bos taurus
Q335SNDFNRHLTPF1Arabidopsis thaliana
Q335PHRQFQHLTPI1Gallus gallus
Q335PHRQFQHLTAI1Xenopus tropicalis
R112---FDRRATSL2Homo sapiens, Bos taurus
R112IRYHSRRVTCL1Arabidopsis thaliana
R112---FDRRTTSL1Mus musculus
R112---FDRRVTCL1Gallus gallus
R112---FDRRVTTL1Xenopus tropicalis
R239ELWNLRMHKKK3Homo sapiens, Mus musculus, Bos taurus
R239PIL-IHKQGSK1Arabidopsis thaliana
R239EIWKLKLHKKK1Gallus gallus
R239EIWKLRLHKKK1Xenopus tropicalis
R332IPHPHRHFQHL2Homo sapiens, Bos taurus
R332IPHPHRQFQHL2Gallus gallus, Xenopus tropicalis
R332IVHSNDFNRHL1Arabidopsis thaliana
R332ISHPHRHFQHL1Mus musculus
R370TPYELRTIDVF1Homo sapiens
R370A---LHPIDFI1Arabidopsis thaliana
R370VPYELRTIDVF1Mus musculus
R370SPHELRTIDVF1Bos taurus
R370TVNELRTVDIF1Gallus gallus
R370MSDELRTVDVF1Xenopus tropicalis
V263LATASVDQTVK3Homo sapiens, Bos taurus, Gallus gallus
V263LLSCGNDHFAR1Arabidopsis thaliana
V263LATASIDQTVK1Mus musculus
V263LASASVDQTVK1Xenopus tropicalis
W203---NIWFCSLD1Homo sapiens
W203NSWKMLY-GMD1Arabidopsis thaliana
W203---KVWFCSLD1Mus musculus
W203---NVWFCSLD1Bos taurus
W203HNVCCWYCSVD1Gallus gallus
W203--WAMWYCSLD1Xenopus tropicalis
Y356IVVGRYPDPNF2Homo sapiens, Bos taurus
Y356IVIGRYISENY1Arabidopsis thaliana
Y356IVVGRYPDPNL1Mus musculus
Y356IVVGRYPDPKF1Gallus gallus
Y356IVVGRYPDPLF1Xenopus tropicalis
Y413ASGMGFNILIW2Gallus gallus, Xenopus tropicalis
Y413ASAMGYHILIW1Homo sapiens
Y413ASGSSRSLFIW1Arabidopsis thaliana
Y413ASTMGYHILIW1Mus musculus
Y413ASVMGYHILVW1Bos taurus

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