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 NEDD4
Gene summary
Basic gene Info.Gene symbolNEDD4
Gene nameneural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase
CytomapUCSC genome browser: 15q
Type of geneprotein-coding
DescriptionE3 ubiquitin-protein ligase NEDD4cell proliferation-inducing gene 53 proteinneural precursor cell expressed developmentally down-regulated protein 4receptor-potentiating factor 1
Modification date20141207
dbXrefs MIM : 602278
Ensembl : ENSG00000069869
HPRD : 03786
Vega : OTTHUMG00000132015
ProteinUniProt: P46934
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NEDD4
BioGPS: 4734
PathwayNCI Pathway Interaction Database: NEDD4
Pathway Commons: NEDD4
ContextiHOP: NEDD4
ligand binding site mutation search in PubMed: NEDD4
UCL Cancer Institute: NEDD4
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006622protein targeting to lysosome17116753
GO:0007041lysosomal transport18544533
GO:0010766negative regulation of sodium ion transport10642508
GO:0016567protein ubiquitination18305167
GO:0031623receptor internalization18544533
GO:0032801receptor catabolic process18544533
GO:0034765regulation of ion transmembrane transport17289006
GO:0042391regulation of membrane potential17289006
GO:0042787protein ubiquitination involved in ubiquitin-dependent protein catabolic process20086093
GO:0042921glucocorticoid receptor signaling pathway8649367
GO:0045732positive regulation of protein catabolic process14973438
GO:0046824positive regulation of nucleocytoplasmic transport17218261
GO:0050847progesterone receptor signaling pathway8649367
GO:1901016regulation of potassium ion transmembrane transporter activity17289006

Ligand binding site mutations for NEDD4
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 NEDD4
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 NEDD4 from PDB

Differential gene expression and gene-gene network for NEDD4
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 NEDD4 and the right PPI network was created from samples without mutations in the LBS of NEDD4. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for NEDD4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0022548Keloid3Biomarker, GeneticVariation
umls:C0151744Myocardial Ischemia1Biomarker

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

Pharmacological information for NEDD4
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 NEDD4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of NEDD4
Multiple alignments for P46934 in multiple species
LBSAA sequence# speciesSpecies

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