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 SDCBP
Gene summary
Basic gene Info.Gene symbolSDCBP
Gene namesyndecan binding protein (syntenin)
CytomapUCSC genome browser: 8q12
Type of geneprotein-coding
Descriptionmelanoma differentiation associated protein-9melanoma differentiation-associated protein 9pro-TGF-alpha cytoplasmic domain-interacting protein 18scaffold protein Pbp1syndecan-binding protein 1syntenin-1
Modification date20141207
dbXrefs MIM : 602217
Ensembl : ENSG00000137575
HPRD : 03741
Vega : OTTHUMG00000164303
ProteinUniProt: O00560
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SDCBP
BioGPS: 6386
PathwayNCI Pathway Interaction Database: SDCBP
Pathway Commons: SDCBP
ContextiHOP: SDCBP
ligand binding site mutation search in PubMed: SDCBP
UCL Cancer Institute: SDCBP
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0042327positive regulation of phosphorylation18256285

Ligand binding site mutations for SDCBP

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 SDCBP
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 SDCBP from PDB

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


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

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

Pharmacological information for SDCBP
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 SDCBP go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (ASN,GLU,TYR,LYS,VAL)1v1tBV209
IIIPeptide ligand (GLU,PHE,TYR,ALA)1yboBV209
IIIPeptide ligand (ASP,SER,VAL,PHE)1obxAV209 A255
IIIPeptide ligand (ASN,GLU,PHE,TYR,ALA)1obyAV209 A255
IIIPeptide ligand (THR,ASN,GLU,PHE,TYR,ALA)1obyBV209 A255
IIIPeptide ligand (ASP,SER,VAL,PHE)1obzAV209 A255
IIIPeptide ligand (ASN,GLU,TYR,LYS,VAL)1v1tAV209 A255
IIIPeptide ligand (ASN,GLU,PHE,TYR,PHE)1w9eAV209 A255
IIIPeptide ligand (ASN,GLU,PHE,TYR,PHE)1w9eBV209 A255
IIIPeptide ligand (ASN,GLU,TYR,TYR,VAL)1w9oAV209 A255
IIIPeptide ligand (ASN,GLU,TYR,TYR,VAL)1w9oBV209 A255
IIIPeptide ligand (ASN,GLU,PHE,ALA,PHE)1w9qBV209 A255
IIIPeptide ligand (THR,ASN,GLU,PHE,TYR,ALA)1yboAV209 A255

Conservation information for LBS of SDCBP
Multiple alignments for O00560 in multiple species
LBSAA sequence# speciesSpecies
A255KDAQIADILST2Mus musculus, Rattus norvegicus
A255KDSQIADILST1Homo sapiens
C239TDHHICEINGQ2Mus musculus, Rattus norvegicus
C239TEHNICEINGQ1Homo sapiens
D251VIGLKDAQIAD2Mus musculus, Rattus norvegicus
D251VIGLKDSQIAD1Homo sapiens
E240DHHICEINGQN2Mus musculus, Rattus norvegicus
E240EHNICEINGQN1Homo sapiens
F211SGHVGFIFKSG2Mus musculus, Rattus norvegicus
F211TGHVGFIFKNG1Homo sapiens
F213HVGFIFKSGKI2Mus musculus, Rattus norvegicus
F213HVGFIFKNGKI1Homo sapiens
G126QDGKIGLRLKS3Homo sapiens, Mus musculus, Rattus norvegicus
G210SSGHVGFIFKS2Mus musculus, Rattus norvegicus
G210STGHVGFIFKN1Homo sapiens
H175SSDKAHKVLKQ3Homo sapiens, Mus musculus, Rattus norvegicus
H208KDSSGHVGFIF2Mus musculus, Rattus norvegicus
H208KDSTGHVGFIF1Homo sapiens
I125DQDGKIGLRLK3Homo sapiens, Mus musculus, Rattus norvegicus
I212GHVGFIFKSGK2Mus musculus, Rattus norvegicus
I212GHVGFIFKNGK1Homo sapiens
I254LKDAQIADILS2Mus musculus, Rattus norvegicus
I254LKDSQIADILS1Homo sapiens
K124KDQDGKIGLRL3Homo sapiens, Mus musculus, Rattus norvegicus
K214VGFIFKSGKIT2Mus musculus, Rattus norvegicus
K214VGFIFKNGKIT1Homo sapiens
L127DGKIGLRLKSI2Homo sapiens, Mus musculus
L127DGKIGLRLKSV1Rattus norvegicus
L258QIADILSTAGT2Mus musculus, Rattus norvegicus
L258QIADILSTSGT1Homo sapiens
N245EINGQNVIGLK3Homo sapiens, Mus musculus, Rattus norvegicus
Q142FVQLVQANSPA3Homo sapiens, Mus musculus, Rattus norvegicus
R128GKIGLRLKSID2Homo sapiens, Mus musculus
R128GKIGLRLKSVD1Rattus norvegicus
S252IGLKDAQIADI2Mus musculus, Rattus norvegicus
S252IGLKDSQIADI1Homo sapiens
V209DSSGHVGFIFK2Mus musculus, Rattus norvegicus
V209DSTGHVGFIFK1Homo sapiens
V222KITSIVKDSSA3Homo sapiens, Mus musculus, Rattus norvegicus

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