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 NME3
Gene summary
Basic gene Info.Gene symbolNME3
Gene nameNME/NM23 nucleoside diphosphate kinase 3
CytomapUCSC genome browser: 16q13.3
Type of geneprotein-coding
DescriptionNDK 3NDP kinase 3NDP kinase Cnon-metastatic cells 3, protein expressed innucleoside diphosphate kinase 3nucleoside diphosphate kinase C
Modification date20141207
dbXrefs MIM : 601817
Ensembl : ENSG00000103024
HPRD : 03488
Vega : OTTHUMG00000128635
ProteinUniProt: Q13232
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NME3
BioGPS: 4832
PathwayNCI Pathway Interaction Database: NME3
Pathway Commons: NME3
ContextiHOP: NME3
ligand binding site mutation search in PubMed: NME3
UCL Cancer Institute: NME3
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

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

Ligand binding site mutations for NME3

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 NME3
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 NME3 from PDB

Differential gene expression and gene-gene network for NME3
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 NME3 and the right PPI network was created from samples without mutations in the LBS of NME3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for NME3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for NME3
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 NME3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of NME3
Multiple alignments for Q13232 in multiple species
LBSAA sequence# speciesSpecies
F77LRERPFYGRLV1Homo sapiens
F77LSAKSFFPNLI1Arabidopsis thaliana
F77LREKPFYSRLV1Mus musculus
G130FCIEVGKNLIH1Homo sapiens
G130LAVQTGRNIVH1Arabidopsis thaliana
G130FCMEVGKNVIH1Mus musculus
K29TFLAVKPDGVQ2Homo sapiens, Mus musculus
K29TYIMVKPDGIQ1Arabidopsis thaliana
L72EHYAELRERPF1Homo sapiens
L72EHYKDLSAKSF1Arabidopsis thaliana
L72EHYVELREKPF1Mus musculus
L81PFYGRLVKYMA1Homo sapiens
L81SFFPNLIEYIT1Arabidopsis thaliana
L81PFYSRLVKYMS1Mus musculus
N132IEVGKNLIHGS1Homo sapiens
N132VQTGRNIVHGS1Arabidopsis thaliana
N132MEVGKNVIHGS1Mus musculus
R105VVRTSRALIGA1Homo sapiens
R105VVASARKLIGK1Arabidopsis thaliana
R105VVHASRALIGA1Mus musculus
R122PPGTIRGDFCI1Homo sapiens
R122EPGTIRGDLAV1Arabidopsis thaliana
R122MPGTIRGDFCM1Mus musculus
T111ALIGATNPADA1Homo sapiens
T111KLIGKTDPLQA1Arabidopsis thaliana
T111ALIGATDPGDA1Mus musculus
V129DFCIEVGKNLI1Homo sapiens
V129DLAVQTGRNIV1Arabidopsis thaliana
V129DFCMEVGKNVI1Mus musculus
Y69LLREHYAELRE1Homo sapiens
Y69LAEEHYKDLSA1Arabidopsis thaliana
Y69LLREHYVELRE1Mus musculus

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