mutLBSgeneDB

mutLBSgeneDB
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 NT5M

Gene summary

Basic gene Info.	Gene symbol	NT5M
	Gene name	5',3'-nucleotidase, mitochondrial
	Synonyms	dNT-2\|dNT2\|mdN
	Cytomap	UCSC genome browser: 17p11.2
	Type of gene	protein-coding
	RefGenes	NM_020201.3,
	Description	5' nucleotidase, mitochondrial5'(3')-deoxyribonucleotidase, mitochondrial5(3)-deoxyribonucleotidasedeoxy-5'-nucleotidase 2mitochondrial 5' nucleotidase
	Modification date	20141207
dbXrefs	MIM : 605292
	HGNC : HGNC
	Ensembl : ENSG00000205309
	HPRD : 12009
	Vega : OTTHUMG00000059277
Protein	UniProt: Q9NPB1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NT5M
	BioGPS: 56953
Pathway	NCI Pathway Interaction Database: NT5M
	KEGG: NT5M
	REACTOME: NT5M
	Pathway Commons: NT5M
Context	iHOP: NT5M
	ligand binding site mutation search in PubMed: NT5M
	UCL Cancer Institute: NT5M
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

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

GO ID

GO Term

PubMed ID

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Ligand binding site mutations for NT5M

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

LBS	AAchange of nsSNV	Cancer type	# samples
T130	C129F	COAD	1
W96	W96C	COAD	1
W96	W96L	LUAD	1
P132	P132R	UCEC	1

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 NT5M

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.

LBS	AAchange of nsSNV	Relative stability change
P132	P132R	-0.82271853
T130	C129F	-0.74644807
W96	W96C	-0.58236369
W96	W96L	-0.20708006

(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 NT5M from PDB

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Differential gene expression and gene-gene network for NT5M

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 NT5M and the right PPI network was created from samples without mutations in the LBS of NT5M. 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 NT5M

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for NT5M

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 status	DrugBank ID	Name	Type	Drug structure
Experimental	DB02217	Dpb-T	Small molecule
Experimental	DB04672	cyclic 3',5'-thymidine monophosphate	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NT5M go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
DRM		1-TRANS-(2-PHOSPHONOMETHOXYCYCLOPENTYL)URACIL	1q92	A	P132
PO4		PHOSPHATE ION	1mh9	A	T130
PO4		PHOSPHATE ION	1q91	A	T130
U2P		URIDINE-2'-PHOSPHATE	1z4j	A	T130 P132
DGP		2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	1z4p	X	W96
D4M		2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-MONOPHOSPHATE	1z4q	A	W96
0BT		1-{2-DEOXY-3,5-O-[(4-IODOPHENYL)(PHOSPHONO) METHYLIDENE]-BETA-D-THREO-PENTOFURANOSYL}-5- METHYLPYRIMIDINE-2,4(1H,3H)-DIONE	4l6c	A	W96
2JW		1-{2-DEOXY-3,5-O-[(4-NITROPHENYL)(PHOSPHONO) METHYLIDENE]-BETA-D-THREO-PENTOFURANOSYL}-5- METHYLPYRIMIDINE-2,4(1H,3H)-DIONE	4nfl	A	W96
2O2		1-{2-DEOXY-3,5-O-[PHENYL(PHOSPHONO)METHYLIDENE]-BETA-D- THREO-PENTOFURANOSYL}-5-[(E)-2- PHOSPHONOETHENYL]PYRIMIDINE-2,4(1H,3H)-DIONE	4yik	A	W96
DPB		DPB-T	1q91	A	W96 P132
TMP		DTMP	1z4l	A	W96 P132
ATM		3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE	2jau	A	W96 P132
BVP		BVDU-MP	2jaw	A	W96 P132
2E2		1-{3,5-O-[(4-CARBOXYPHENYL)(PHOSPHONO)METHYLIDENE]-2- DEOXY-BETA-D-THREO-PENTOFURANOSYL}-5-METHYLPYRIMIDINE- 2,4(1H,3H)-DIONE	4mwo	A	W96 P132
UMP		DUMP	1z4i	A	W96 T130 P132
T3P		THYMIDINE-3'-PHOSPHATE	1z4k	A	W96 T130 P132
U5P		UMP	1z4m	A	W96 T130 P132

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Conservation information for LBS of NT5M

Multiple alignments for Q9NPB1 in multiple species

LBS

AA sequence

# species

Species