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 NEK2
Gene summary
Basic gene Info.Gene symbolNEK2
Gene nameNIMA-related kinase 2
SynonymsHsPK21|NEK2A|NLK1|PPP1R111|RP67
CytomapUCSC genome browser: 1q32.3
Type of geneprotein-coding
RefGenesNM_001204182.1,
NM_001204183.1,NM_002497.3,
DescriptionNIMA (never in mitosis gene a)-related kinase 2nimA-like protein kinase 1nimA-related protein kinase 2protein phosphatase 1, regulatory subunit 111serine/threonine-protein kinase Nek2
Modification date20141222
dbXrefs MIM : 604043
HGNC : HGNC
Ensembl : ENSG00000117650
HPRD : 04953
Vega : OTTHUMG00000037121
ProteinUniProt: P51955
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NEK2
BioGPS: 4751
PathwayNCI Pathway Interaction Database: NEK2
KEGG: NEK2
REACTOME: NEK2
Pathway Commons: NEK2
ContextiHOP: NEK2
ligand binding site mutation search in PubMed: NEK2
UCL Cancer Institute: NEK2
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0006468protein phosphorylation21076410
GO:0007059chromosome segregation14978040
GO:0046777protein autophosphorylation17626005
GO:0051299centrosome separation18086858


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Ligand binding site mutations for NEK2
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
Y12Y12CBRCA1
G92G92VUCEC1
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 NEK2
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
Y12Y12C-0.61953003
G92G92V-0.23782219
(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 NEK2 from PDB

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Differential gene expression and gene-gene network for NEK2
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 NEK2 and the right PPI network was created from samples without mutations in the LBS of NEK2. 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 NEK2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for NEK2
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
ExperimentalDB071805-[(Z)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDESmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NEK2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
5Z55-[(Z)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE2javAG92
VGK4-[2-AMINO-5-(3,4,5-TRIMETHOXYPHENYL)PYRIDIN-3-YL]BENZOIC ACID2wqoAG92
XK34-[3-AMINO-6-(3-ETHYLTHIOPHEN-2-YL)PYRAZIN-2-YL]CYCLOHEXANE-1-CARBOXYLIC ACID2xk3AG92
OL24-[3-AMINO-6-(3,4,5-TRIMETHOXYPHENYL)PYRAZIN-2-YL]-2-ETHOXYBENZOIC ACID2xk4AG92
EQHCIS-4-[3-AMINO-6-(3-CYCLOPROPYLTHIOPHEN-2-YL)PYRAZIN-2-YL]CYCLOHEXANECARBOXYLIC ACID2xk6AG92
30E(3R,4R)-1-[3-AMINO-6-(3,4,5-TRIMETHOXYPHENYL)PYRAZIN-2-YL]-3-ETHYLPIPERIDINE-4-CARBOXYLICACID2xk7AG92
5R14-[3-AMINO-6-(3,4,5-TRIMETHOXYPHENYL)PYRAZIN-2-YL]-2-METHOXYBENZOIC ACID2xk8AG92
4VQ4-[3-AMINO-6-(3,4,5-TRIMETHOXYPHENYL)PYRAZIN-2-YL]-2-METHYLBENZOIC ACID2xkcAG92
T3M4-[3-AMINO-6-(3,4,5-TRIMETHOXYPHENYL)PYRAZIN-2-YL]BENZOIC ACID2xkdAG92
WI21-[3-AMINO-6-(3-METHOXYPHENYL)PYRAZIN-2-YL]PIPERIDINE-4-CARBOXYLIC ACID2xkeAG92
BX11-[3-AMINO-6-(3,4,5-TRIMETHOXYPHENYL)PYRAZIN-2-YL]PIPERIDINE-4-CARBOXYLIC ACID2xkfAG92
WGZ5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-3-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}THIOPHENE-2-CARBOXAMIDE2xnmAG92
4305-(1H-BENZIMIDAZOL-1-YL)-3-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}THIOPHENE-2-CARBOXAMIDE2xnnAG92
WCX4-{5-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE2xnpAG92
GGY4-(2-AMINO-5-{4-[(DIMETHYLAMINO)METHYL]THIOPHEN-2-YL}PYRIDIN-3-YL)-2-{[(1R,2Z)-4,4,4-TRIFLUORO-1-METHYLBUT-2-EN-1-YL]OXY}BENZAMIDE4afeAY12 G92


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Conservation information for LBS of NEK2
Multiple alignments for P51955 in multiple species
LBSAA sequence# speciesSpecies
A145RDLKPANVFLD2Homo sapiens, Mus musculus
A145RDIKPANIFLD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C22GSYGRCQKIRR2Homo sapiens, Mus musculus
C22GSFGRIYKVQR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C89IVMEYCEGGDL2Homo sapiens, Mus musculus
C89LYMEYCGHGDL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D159NVKLGDFGLAR2Homo sapiens, Mus musculus
D159SVKLGDFGLSK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D93YCEGGDLASVI2Homo sapiens, Mus musculus
D93YCGHGDLANLI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E87LYIVMEYCEGG2Homo sapiens, Mus musculus
E87INLYMEYCGHG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E90VMEYCEGGDLA2Homo sapiens, Mus musculus
E90YMEYCGHGDLA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F148KPANVFLDGKQ1Homo sapiens
F148KPANIFLDENN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F148KPANVFLDSKH1Mus musculus
G15VLYTIGTGSYG1Homo sapiens
G15ILECIGHGSFG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G15VLHSIGTGSYG1Mus musculus
G158QNVKLGDFGLA1Homo sapiens
G158NSVKLGDFGLS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G158HNVKLGDFGLA1Mus musculus
G17YTIGTGSYGRC1Homo sapiens
G17ECIGHGSFGRI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G17HSIGTGSYGRC1Mus musculus
G92EYCEGGDLASV2Homo sapiens, Mus musculus
G92EYCGHGDLANL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I14EVLYTIGTGSY1Homo sapiens
I14KILECIGHGSF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I14EVLHSIGTGSY1Mus musculus
K37KILVWKELDYG2Homo sapiens, Mus musculus
K37ALLAQKEIHFG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L162LGDFGLARILN2Homo sapiens, Mus musculus
L162LGDFGLSKLLD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M86TLYIVMEYCEG2Homo sapiens, Mus musculus
M86VINLYMEYCGH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N146DLKPANVFLDG1Homo sapiens
N146DIKPANIFLDE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N146DLKPANVFLDS1Mus musculus
S18TIGTGSYGRCQ1Homo sapiens
S18CIGHGSFGRIY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S18SIGTGSYGRCQ1Mus musculus
S96GGDLASVITKG1Homo sapiens
S96HGDLANLIQRY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S96GGDLASVISKG1Mus musculus
V35DGKILVWKELD2Homo sapiens, Mus musculus
V35DGALLAQKEIH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V68KHPNIVRYYDR1Homo sapiens
V68KHPNIVQYCGE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V68KHPNIVSYYDR1Mus musculus
Y12DYEVLYTIGTG1Homo sapiens
Y12KYKILECIGHG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y12DYEVLHSIGTG1Mus musculus
Y19IGTGSYGRCQK2Homo sapiens, Mus musculus
Y19IGHGSFGRIYK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y70PNIVRYYDRII1Homo sapiens
Y70PNIVQYCGEEL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y70PNIVSYYDRII1Mus musculus
Y88YIVMEYCEGGD2Homo sapiens, Mus musculus
Y88NLYMEYCGHGD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)


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