mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 NT5C2
Gene summary
Basic gene Info.Gene symbolNT5C2
Gene name5'-nucleotidase, cytosolic II
SynonymsGMP|NT5B|PNT5|SPG45|SPG65|cN-II
CytomapUCSC genome browser: 10q24.32
Type of geneprotein-coding
RefGenesNM_001134373.2,
NM_012229.4,
Description5'-nucleotidase (purine), cytosolic type BIMP-specific 5'-NTcytosolic 5'-nucleotidase IIcytosolic purine 5'-nucleotidasepurine 5' nucleotidase
Modification date20141207
dbXrefs MIM : 600417
HGNC : HGNC
Ensembl : ENSG00000076685
HPRD : 02686
Vega : OTTHUMG00000018981
ProteinUniProt: P49902
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NT5C2
BioGPS: 22978
PathwayNCI Pathway Interaction Database: NT5C2
KEGG: NT5C2
REACTOME: NT5C2
Pathway Commons: NT5C2
ContextiHOP: NT5C2
ligand binding site mutation search in PubMed: NT5C2
UCL Cancer Institute: NT5C2
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


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Ligand binding site mutations for NT5C2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
Q453A451VCOAD1
K362K361NCOAD1
Q420R422CCOAD1
S445S443NLUAD1
K292R291QSTAD1
R456R456CUCEC1
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 NT5C2
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
K292R291Q-1.5497304
R456R456C-1.500459
K362K361N-0.77387376
Q453A451V-0.76486668
Q420R422C-0.65027653
S445S443N-0.46366854
(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 NT5C2 from PDB

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Differential gene expression and gene-gene network for NT5C2
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 NT5C2 and the right PPI network was created from samples without mutations in the LBS of NT5C2. 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 NT5C2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1961102Precursor Cell Lymphoblastic Leukemia-Lymphoma3Biomarker
umls:C2825055Recurrence1Biomarker

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

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Pharmacological information for NT5C2
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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
Approved|nutraceuticalDB00171Adenosine triphosphateSmall molecule
ApprovedDB00811RibavirinSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NT5C2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IMPIMP2xcvAK292
IMPIMP2xcwAK292
DG2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE2xjbAK292
5GPGMP RESIDUE2xjcAK292
PO4PHOSPHATE ION2xjdAK292
U5PUMP2xjeAK292
DG22,3-BISPHOSPHOGLYCERATE2xcvAK362
DG22,3-BISPHOSPHOGLYCERATE2xjfAK362
B4PDIADENOSINE TETRAPHOSPHATE2xjcAK362 Q453
53O1-(BIPHENYL-3-YL)-1H-IMIDAZOLE5cqzAQ420 S445
53O1-(BIPHENYL-3-YL)-1H-IMIDAZOLE5cqzBQ420 S445
ADNADENOSINE2jc9AQ453
11H9,10-DIOXO-9,10-DIHYDROANTHRACENE-2,6-DISULFONIC ACID4h4bAQ453
ATPATP2xcwAQ453 R456
DTPDATP(4-)2xjbAQ453 R456
ATPATP2xjdAQ453 R456
ATPATP2xjeAQ453 R456


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Conservation information for LBS of NT5C2
Multiple alignments for P49902 in multiple species
LBSAA sequence# speciesSpecies
D145KFIQRDDTERF3Homo sapiens, Bos taurus, Mus musculus
D145KFIQRDDTDRF2Xenopus tropicalis, Gallus gallus
D206VRDAVDWVHYK5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
D351ILYIGDHIFGD5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
D52KCFGFDMDYTL5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
D54FGFDMDYTLAV5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
F127AHGFNFIRGPE3Homo sapiens, Bos taurus, Mus musculus
F127AHGFNFMRGPE1Xenopus tropicalis
F127AHGFNFLRGPE1Gallus gallus
F157ILNTLFNLPET5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
F354IGDHIFGDILK5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
H209AVDWVHYKGSL5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
H428IKKVTHDMDMC5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
I152TERFYILNTLF3Homo sapiens, Bos taurus, Mus musculus
I152TDRFYILNTLF2Xenopus tropicalis, Gallus gallus
K215YKGSLKEKTVE4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
K215YKGSLKEKTLE1Gallus gallus
K292LVDARKPLFFG5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
K362ILKSKKRQGWR5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
L358IFGDILKSKKR5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
L476YPFSYLFRAAH5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
M432THDMDMCYGMM5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
M436DMCYGMMGSLF5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
M53CFGFDMDYTLA5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
N154RFYILNTLFNL5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
N250VFLATNSDYKY3Homo sapiens, Bos taurus, Mus musculus
N250VFLVTNSDYKY2Xenopus tropicalis, Gallus gallus
P293VDARKPLFFGE5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
Q420DISSIQRRIKK5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
Q453TLFASQVMRYA5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
R129GFNFIRGPETR3Homo sapiens, Bos taurus, Mus musculus
R129GFNFMRGPEIR1Xenopus tropicalis
R129GFNFLRGPETR1Gallus gallus
R144NKFIQRDDTER3Homo sapiens, Bos taurus, Mus musculus
R144NKFIQRDDTDR2Xenopus tropicalis, Gallus gallus
R202MFQDVRDAVDW5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
R39RVFVNRSLAME5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
R446FRSGSRQTLFA5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
R456ASQVMRYADLY5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
R478FSYLFRAAHVL5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
S251FLATNSDYKYT3Homo sapiens, Bos taurus, Mus musculus
S251FLVTNSDYKYT2Xenopus tropicalis, Gallus gallus
S40VFVNRSLAMEK5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
S445LFRSGSRQTLF5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
T147IQRDDTERFYI3Homo sapiens, Bos taurus, Mus musculus
T147IQRDDTDRFYI2Xenopus tropicalis, Gallus gallus
T249KVFLATNSDYK3Homo sapiens, Bos taurus, Mus musculus
T249KVFLVTNSDYK2Xenopus tropicalis, Gallus gallus
Y210VDWVHYKGSLK5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus
Y457SQVMRYADLYA5Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus


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