mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

	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 NUDT5

Gene summary

Basic gene Info.	Gene symbol	NUDT5
	Gene name	nudix (nucleoside diphosphate linked moiety X)-type motif 5
	Synonyms	YSA1\|YSA1H\|YSAH1\|hYSAH1
	Cytomap	UCSC genome browser: 10p14
	Type of gene	protein-coding
	RefGenes	NM_014142.2,
	Description	8-oxo-dGDP phosphataseADP-sugar pyrophosphatase
	Modification date	20141207
dbXrefs	MIM : 609230
	HGNC : HGNC
	Ensembl : ENSG00000165609
	HPRD : 14851
Protein	UniProt: Q9UKK9 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NUDT5
	BioGPS: 11164
Pathway	NCI Pathway Interaction Database: NUDT5
	KEGG: NUDT5
	REACTOME: NUDT5
	Pathway Commons: NUDT5
Context	iHOP: NUDT5
	ligand binding site mutation search in PubMed: NUDT5
	UCL Cancer Institute: NUDT5
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
GO:0009191	ribonucleoside diphosphate catabolic process	18462755

Top

Ligand binding site mutations for NUDT5

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
E166	G165V	OV	1
W46	W46R	SKCM	1
R51	T53A	STAD	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.

Top

Protein structure related information for NUDT5

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
R51	T53A	-1.2642045
W46	W46R	-0.52256816
E166	G165V	-0.11594932

(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 NUDT5 from PDB

Top

Differential gene expression and gene-gene network for NUDT5

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 NUDT5 and the right PPI network was created from samples without mutations in the LBS of NUDT5. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

Top

Phenotype information for NUDT5

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

Top

Pharmacological information for NUDT5

Drug information targeting mutLBSgene (Approved drugs only)

Drug status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NUDT5 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
MG		MAGNESIUM(2+)	2dsc	A	E166
MG		MAGNESIUM(2+)	2dsd	A	E166
AMP		AMP	2dsd	A	E166
MG		MAGNESIUM(2+)	2dsd	B	E166
MG		MAGNESIUM(2+)	2dsd	B	E166
MN		MANGANESE(2+)	3ac9	B	E166
MN		MANGANESE(2+)	3aca	A	E166
MN		MANGANESE(2+)	3aca	B	E166
MG		MAGNESIUM(2+)	3bm4	B	E166
APR		ADP-RIBOSE	2dsc	B	R51
8GD		8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-DIPHOSPHATE	3ac9	A	R51
8DD		8-OXO-7,8-DIHYDRO-2'-DEOXY-ADENOSINE-5'-DIPHOSPHATE	3aca	A	R51
8OG		8-HYDROXYDEOXYGUANOSINE 5'-MONOPHOSPHATE	3l85	B	R51
APR		ADP-RIBOSE	2dsc	A	R51 E166
AMP		AMP	2dsd	B	R51 E166
8GD		8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-DIPHOSPHATE	3ac9	B	R51 E166
8DD		8-OXO-7,8-DIHYDRO-2'-DEOXY-ADENOSINE-5'-DIPHOSPHATE	3aca	B	R51 E166
ADV		ALPHA-BETA METHYLENE ADP-RIBOSE	3bm4	A	R51 E166
ADV		ALPHA-BETA METHYLENE ADP-RIBOSE	3bm4	B	R51 E166
APR		ADP-RIBOSE	2dsc	A	W46
APR		ADP-RIBOSE	2dsc	B	W46
AMP		AMP	2dsd	A	W46
AMP		AMP	2dsd	B	W46
8GD		8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-DIPHOSPHATE	3ac9	A	W46
8GD		8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-DIPHOSPHATE	3ac9	B	W46
8DD		8-OXO-7,8-DIHYDRO-2'-DEOXY-ADENOSINE-5'-DIPHOSPHATE	3aca	A	W46
8DD		8-OXO-7,8-DIHYDRO-2'-DEOXY-ADENOSINE-5'-DIPHOSPHATE	3aca	B	W46
ADV		ALPHA-BETA METHYLENE ADP-RIBOSE	3bm4	A	W46
ADV		ALPHA-BETA METHYLENE ADP-RIBOSE	3bm4	B	W46
8OG		8-HYDROXYDEOXYGUANOSINE 5'-MONOPHOSPHATE	3l85	A	W46
8OG		8-HYDROXYDEOXYGUANOSINE 5'-MONOPHOSPHATE	3l85	B	W46

Top

Conservation information for LBS of NUDT5

Multiple alignments for Q9UKK9 in multiple species

LBS	AA sequence	# species	Species
A96	CIEFPAGLIDD	1	Homo sapiens
A96	CLELPAGLIDA	1	Caenorhabditis elegans
A96	CLEFPAGFIED	1	Mus musculus
A96	CLEFPAGLIED	1	Rattus norvegicus
A96	CIEMPAGLIDA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A96	CIEIPAGLVDS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D133	PAVCMDPGLSN	3	Homo sapiens, Mus musculus, Rattus norvegicus
D133	KLCFLDPGLTD	1	Caenorhabditis elegans
D133	PTVFNDPGFTN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D133	TVMYNDPGLTN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E112	AAALRELEEET	3	Homo sapiens, Mus musculus, Rattus norvegicus
E112	QAAIRELKEET	1	Caenorhabditis elegans
E112	TAALRELKEET	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E112	DAAIRELREET	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E115	LRELEEETGYK	3	Homo sapiens, Mus musculus, Rattus norvegicus
E115	IRELKEETGYV	1	Caenorhabditis elegans
E115	LRELKEETGYS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E115	IRELREETGYV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E116	RELEEETGYK-	3	Homo sapiens, Mus musculus, Rattus norvegicus
E116	RELKEETGYVS	1	Caenorhabditis elegans
E116	RELKEETGYS-	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E116	RELREETGYV-	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E166	KPGDGEFVEVI	2	Homo sapiens, Rattus norvegicus
E166	VLDSTESIEVL	1	Caenorhabditis elegans
E166	KPGDGEFMEVI	1	Mus musculus
E166	QLEDNEFIECF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E166	QLDDGEYIENF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E47	KTRTWETVKLT	2	Mus musculus, Rattus norvegicus
E47	KTRTWESVKRT	1	Homo sapiens
E47	QVGVWQSVHRN	1	Caenorhabditis elegans
E47	KEREWDSAVRT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E47	KIRFWEMAERT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G135	VCMDPGLSNCT	3	Homo sapiens, Mus musculus, Rattus norvegicus
G135	CFLDPGLTDDS	1	Caenorhabditis elegans
G135	VFNDPGFTNTN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G135	MYNDPGLTNAN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G97	IEFPAGLIDDG	1	Homo sapiens
G97	LELPAGLIDAG	1	Caenorhabditis elegans
G97	LEFPAGFIEDG	1	Mus musculus
G97	LEFPAGLIEDG	1	Rattus norvegicus
G97	IEMPAGLIDAG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G97	IEIPAGLVDSK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L98	EFPAGLIDDGE	1	Homo sapiens
L98	ELPAGLIDAGE	1	Caenorhabditis elegans
L98	EFPAGFIEDGE	1	Mus musculus
L98	EFPAGLIEDGE	1	Rattus norvegicus
L98	EMPAGLIDAGE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L98	EIPAGLVDSKE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M132	SPAVCMDPGLS	3	Homo sapiens, Mus musculus, Rattus norvegicus
M132	SKLCFLDPGLT	1	Caenorhabditis elegans
M132	SPTVFNDPGFT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M132	TTVMYNDPGLT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P134	AVCMDPGLSNC	3	Homo sapiens, Mus musculus, Rattus norvegicus
P134	LCFLDPGLTDD	1	Caenorhabditis elegans
P134	TVFNDPGFTNT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P134	VMYNDPGLTNA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q82	IVLVKQFRPPM	2	Homo sapiens, Rattus norvegicus
Q82	IVLVKQYRIPC	1	Caenorhabditis elegans
Q82	VILVKQFRPPM	1	Mus musculus
Q82	ILLQKQFRPPV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q82	VLCQKQFRPPI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R111	EAAALRELEEE	3	Homo sapiens, Mus musculus, Rattus norvegicus
R111	QQAAIRELKEE	1	Caenorhabditis elegans
R111	DTAALRELKEE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R111	EDAAIRELREE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R51	WETVKLTTRK-	2	Mus musculus, Rattus norvegicus
R51	WESVKRTTRK-	1	Homo sapiens
R51	WQSVHRNTKPV	1	Caenorhabditis elegans
R51	WDSAVRTTRS-	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R51	WEMAERTTRS-	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R84	LVKQFRPPMGG	2	Homo sapiens, Rattus norvegicus
R84	LVKQYRIPCGK	1	Caenorhabditis elegans
R84	LVKQFRPPMGS	1	Mus musculus
R84	LQKQFRPPVEG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R84	CQKQFRPPIGK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T45	TGKTRTWETVK	2	Mus musculus, Rattus norvegicus
T45	TGKTRTWESVK	1	Homo sapiens
T45	TGQVGVWQSVH	1	Caenorhabditis elegans
T45	NGKEREWDSAV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T45	KGKIRFWEMAE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V29	SEGKWVKFEKT	2	Mus musculus, Rattus norvegicus
V29	SEGKWVKLEKT	1	Homo sapiens
V29	WNGKWIQTRQV	1	Caenorhabditis elegans
V29	SDCKWIGLQKI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V29	QDAKWTSLKKI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
W28	-SEGKWVKFEK	2	Mus musculus, Rattus norvegicus
W28	-SEGKWVKLEK	1	Homo sapiens
W28	VWNGKWIQTRQ	1	Caenorhabditis elegans
W28	TSDCKWIGLQK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
W28	NQDAKWTSLKK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
W46	GKTRTWETVKL	2	Mus musculus, Rattus norvegicus
W46	GKTRTWESVKR	1	Homo sapiens
W46	GQVGVWQSVHR	1	Caenorhabditis elegans
W46	GKEREWDSAVR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
W46	GKIRFWEMAER	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)