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 NMT1
Gene summary
Basic gene Info.Gene symbolNMT1
Gene nameN-myristoyltransferase 1
SynonymsNMT
CytomapUCSC genome browser: 17q21.31
Type of geneprotein-coding
RefGenesNM_021079.3,
DescriptionNMT 1alternative, short form NMT-Sglycylpeptide N-tetradecanoyltransferase 1long form, NMT-Lmyristoyl-CoA:protein N-myristoyltransferase 1peptide N-myristoyltransferase 1type I N-myristoyltransferase
Modification date20141207
dbXrefs MIM : 160993
HGNC : HGNC
Ensembl : ENSG00000136448
HPRD : 01187
Vega : OTTHUMG00000180003
ProteinUniProt: P30419
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NMT1
BioGPS: 4836
PathwayNCI Pathway Interaction Database: NMT1
KEGG: NMT1
REACTOME: NMT1
Pathway Commons: NMT1
ContextiHOP: NMT1
ligand binding site mutation search in PubMed: NMT1
UCL Cancer Institute: NMT1
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
GO:0018008N-terminal peptidyl-glycine N-myristoylation25255805


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Ligand binding site mutations for NMT1
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
Y117R115QBRCA1
Q278Q278RCOAD1
I264,T268E266QHNSC1
H272H272YHNSC1
T268R269SLUAD1
N451F450LSKCM1
R255R255HSTAD1
R189R189QUCEC1
Y420,L416A418VUCEC1
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 NMT1
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
R255R255H-1.5446675
R189R189Q-1.2689522
I264E266Q-1.0955078
T268E266Q-1.0955078
T268R269S-1.0578063
Y117R115Q-0.7246757
Q278Q278R-0.51477292
N451F450L-0.50937609
H272H272Y-0.28208705
L416A418V-0.083504166
Y420A418V-0.083504166
(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 NMT1 from PDB

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Differential gene expression and gene-gene network for NMT1
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 NMT1 and the right PPI network was created from samples without mutations in the LBS of NMT1. 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 NMT1
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 NMT1
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
ExperimentalDB03062(1-Methyl-1h-Imidazol-2-Yl)-(3-Methyl-4-{3-[(Pyridin-3-Ylmethyl)-Amino]-Propoxy}-Benzofuran-2-Yl)-MethanoneSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NMT1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
6462,6-DICHLORO-4-(2-PIPERAZIN-1-YLPYRIDIN-4-YL)-N-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)BENZENESULFONAMIDE4c2zAL416 Y420
X55(2R)-3-BENZYL-2-(2-BROMO-4-HYDROXY-5-METHOXYPHENYL)-1,3-THIAZOLIDIN-4-ONE3jtkAR189 L416 Y420 N451
6462,6-DICHLORO-4-(2-PIPERAZIN-1-YLPYRIDIN-4-YL)-N-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)BENZENESULFONAMIDE3iweAR189 Y420
096(2R)-2-{4-HYDROXY-5-METHOXY-2-[3-(4-METHYLPIPERAZIN-1-YL)PROPYL]PHENYL}-3-PYRIDIN-3-YL-1,3-THIAZOLIDIN-4-ONE3iu2AR189 Y420 N451
096(2R)-2-{4-HYDROXY-5-METHOXY-2-[3-(4-METHYLPIPERAZIN-1-YL)PROPYL]PHENYL}-3-PYRIDIN-3-YL-1,3-THIAZOLIDIN-4-ONE3iu2BR189 Y420 N451
MGMAGNESIUM(2+)4c2yAR255
MGMAGNESIUM(2+)4c2yBR255
MGMAGNESIUM(2+)4c2zAR255
MGMAGNESIUM(2+)4c2zBR255
MYAMYRISTOYL-COA3iu1BY117 R255 I264 T268
MYAMYRISTOYL-COA3iweBY117 R255 I264 T268 H272
MYAMYRISTOYL-COA3jtkBY117 R255 I264 T268 H272
MYAMYRISTOYL-COA4c2zAY117 R255 I264 T268 H272
MYAMYRISTOYL-COA4c2zBY117 R255 I264 T268 H272
MYAMYRISTOYL-COA3iu2AY117 R255 T268
MYAMYRISTOYL-COA3iu2BY117 R255 T268
MYAMYRISTOYL-COA3iweAY117 R255 T268
MYAMYRISTOYL-COA3jtkAY117 R255 T268
MYAMYRISTOYL-COA4c2yBY117 R255 T268
MYAMYRISTOYL-COA3iu1AY117 R255 T268 Q278
MYAMYRISTOYL-COA4c2yAY117 R255 T268 Q278
6462,6-DICHLORO-4-(2-PIPERAZIN-1-YLPYRIDIN-4-YL)-N-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)BENZENESULFONAMIDE3iweBY420
6462,6-DICHLORO-4-(2-PIPERAZIN-1-YLPYRIDIN-4-YL)-N-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)BENZENESULFONAMIDE4c2zBY420


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Conservation information for LBS of NMT1
Multiple alignments for P30419 in multiple species
LBSAA sequence# speciesSpecies
A260RSKRVAPVLIR4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
A260RSKRLAPVMIK1Arabidopsis thaliana
A279EGIFQAVYTAG3Homo sapiens, Mus musculus, Rattus norvegicus
A279ENIWQAAYTAG1Arabidopsis thaliana
A279TGIFQAAYTAG1Drosophila melanogaster
C249EINFLCVHKKL4Homo sapiens, Arabidopsis thaliana, Mus musculus, Rattus norvegicus
C249DINFLCVHKKL1Drosophila melanogaster
D183ENYVEDDDNMF3Homo sapiens, Mus musculus, Rattus norvegicus
D183NNYVEDDENMF1Arabidopsis thaliana
D183ENYVEDDDAMF1Drosophila melanogaster
D184NYVEDDDNMFR3Homo sapiens, Mus musculus, Rattus norvegicus
D184NYVEDDENMFR1Arabidopsis thaliana
D184NYVEDDDAMFR1Drosophila melanogaster
D471KFGIGDGNLQY3Homo sapiens, Mus musculus, Rattus norvegicus
D471KFGPGDGQLHY1Arabidopsis thaliana
D471KFGAGDGNLQY1Drosophila melanogaster
E182NENYVEDDDNM3Homo sapiens, Mus musculus, Rattus norvegicus
E182KNNYVEDDENM1Arabidopsis thaliana
E182NENYVEDDDAM1Drosophila melanogaster
F119KRSYQFWDTQP3Homo sapiens, Mus musculus, Rattus norvegicus
F119AKTHKFWETQP1Arabidopsis thaliana
F119-KKFAFWSTQP1Drosophila melanogaster
F188DDDNMFRFDYS3Homo sapiens, Mus musculus, Rattus norvegicus
F188DDENMFRFNYS1Arabidopsis thaliana
F188DDDAMFRFDYQ1Drosophila melanogaster
F190DNMFRFDYSPE3Homo sapiens, Mus musculus, Rattus norvegicus
F190ENMFRFNYSKE1Arabidopsis thaliana
F190DAMFRFDYQPE1Drosophila melanogaster
F247MVEINFLCVHK3Homo sapiens, Mus musculus, Rattus norvegicus
F247MAEINFLCVHK1Arabidopsis thaliana
F247VVDINFLCVHK1Drosophila melanogaster
F277HLEGIFQAVYT3Homo sapiens, Mus musculus, Rattus norvegicus
F277HLENIWQAAYT1Arabidopsis thaliana
F277NLTGIFQAAYT1Drosophila melanogaster
F311LIEVKFSHLSR3Homo sapiens, Mus musculus, Rattus norvegicus
F311LIDVGFSRLGA1Arabidopsis thaliana
F311LVDVRFSHLAR1Drosophila melanogaster
F375EVEHWFYPQEN3Homo sapiens, Mus musculus, Rattus norvegicus
F375DVEHWLLPRED1Arabidopsis thaliana
F375EFRHWFTPKEG1Drosophila melanogaster
F397GEVTDFLSFYT3Homo sapiens, Mus musculus, Rattus norvegicus
F397HDVTDFCSFYT1Arabidopsis thaliana
F397GNITDLTSYYC1Drosophila melanogaster
G284AVYTAGVVLPK3Homo sapiens, Mus musculus, Rattus norvegicus
G284AAYTAGVILPT1Arabidopsis thaliana
G284AAYTAGVVLPT1Drosophila melanogaster
G472FGIGDGNLQYY3Homo sapiens, Mus musculus, Rattus norvegicus
G472FGPGDGQLHYY1Arabidopsis thaliana
G472FGAGDGNLQYY1Drosophila melanogaster
H272ITRRVHLEGIF3Homo sapiens, Mus musculus, Rattus norvegicus
H272VTRRVHLENIW1Arabidopsis thaliana
H272ITRRVNLTGIF1Drosophila melanogaster
H298TCRYWHRSLNP4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
H298TCQYWHRSLNP1Arabidopsis thaliana
I245KKMVEINFLCV3Homo sapiens, Mus musculus, Rattus norvegicus
I245VKMAEINFLCV1Arabidopsis thaliana
I245LKVVDINFLCV1Drosophila melanogaster
I264VAPVLIREITR4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
I264LAPVMIKEVTR1Arabidopsis thaliana
K257KKLRSKRVAPV4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
K257KKLRSKRLAPV1Arabidopsis thaliana
L248VEINFLCVHKK3Homo sapiens, Mus musculus, Rattus norvegicus
L248AEINFLCVHKK1Arabidopsis thaliana
L248VDINFLCVHKK1Drosophila melanogaster
L254CVHKKLRSKRV4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
L254CVHKKLRSKRL1Arabidopsis thaliana
L287TAGVVLPKPVG3Homo sapiens, Mus musculus, Rattus norvegicus
L287TAGVILPTPIT1Arabidopsis thaliana
L287TAGVVLPTPVA1Drosophila melanogaster
L353VVHQLLSRYLK2Mus musculus, Rattus norvegicus
L353VVHQLLTRYLK1Homo sapiens
L353AVTRLLRNYLS1Arabidopsis thaliana
L353KAHKLLEDYLK1Drosophila melanogaster
L416PTHKSLKAAYS3Homo sapiens, Mus musculus, Rattus norvegicus
L416PNYTTLKAAYS1Arabidopsis thaliana
L416PVHKTVRAAYS1Drosophila melanogaster
L474IGDGNLQYYLY3Homo sapiens, Mus musculus, Rattus norvegicus
L474PGDGQLHYYLY1Arabidopsis thaliana
L474AGDGNLQYYLY1Drosophila melanogaster
N179TLLNENYVEDD4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
N179NLLKNNYVEDD1Arabidopsis thaliana
N246KMVEINFLCVH3Homo sapiens, Mus musculus, Rattus norvegicus
N246KMAEINFLCVH1Arabidopsis thaliana
N246KVVDINFLCVH1Drosophila melanogaster
N424AYSFYNVHTQT3Homo sapiens, Mus musculus, Rattus norvegicus
N424AYSYYNVATQT1Arabidopsis thaliana
N424AYSFYNVSTKT1Drosophila melanogaster
N451GFDVFNALDLM3Homo sapiens, Mus musculus, Rattus norvegicus
N451GFDVFNALDVM1Arabidopsis thaliana
N451QMDVYNALDLM1Drosophila melanogaster
P261SKRVAPVLIRE4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
P261SKRLAPVMIKE1Arabidopsis thaliana
Q118SKRSYQFWDTQ3Homo sapiens, Mus musculus, Rattus norvegicus
Q118EAKTHKFWETQ1Arabidopsis thaliana
Q118--KKFAFWSTQ1Drosophila melanogaster
Q18APSLPLMMEGN2Mus musculus, Rattus norvegicus
Q18APPLPQMMEGN1Homo sapiens
Q18PGSVEQKADQI1Arabidopsis thaliana
Q18GQELKQKAKEV1Drosophila melanogaster
Q278LEGIFQAVYTA3Homo sapiens, Mus musculus, Rattus norvegicus
Q278LENIWQAAYTA1Arabidopsis thaliana
Q278LTGIFQAAYTA1Drosophila melanogaster
R189DDNMFRFDYSP3Homo sapiens, Mus musculus, Rattus norvegicus
R189DENMFRFNYSK1Arabidopsis thaliana
R189DDAMFRFDYQP1Drosophila melanogaster
R255VHKKLRSKRVA4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
R255VHKKLRSKRLA1Arabidopsis thaliana
R258KLRSKRVAPVL4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
R258KLRSKRLAPVM1Arabidopsis thaliana
S256HKKLRSKRVAP4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
S256HKKLRSKRLAP1Arabidopsis thaliana
S405FYTLPSTIMNH3Homo sapiens, Mus musculus, Rattus norvegicus
S405FYTLPSTILGN1Arabidopsis thaliana
S405YYCLPSSVMHH1Drosophila melanogaster
T268LIREITRRVHL3Homo sapiens, Mus musculus, Rattus norvegicus
T268MIKEVTRRVHL1Arabidopsis thaliana
T268LIREITRRVNL1Drosophila melanogaster
T282FQAVYTAGVVL3Homo sapiens, Mus musculus, Rattus norvegicus
T282WQAAYTAGVIL1Arabidopsis thaliana
T282FQAAYTAGVVL1Drosophila melanogaster
V181LNENYVEDDDN3Homo sapiens, Mus musculus, Rattus norvegicus
V181LKNNYVEDDEN1Arabidopsis thaliana
V181LNENYVEDDDA1Drosophila melanogaster
V250INFLCVHKKLR5Homo sapiens, Arabidopsis thaliana, Mus musculus, Rattus norvegicus, Drosophila melanogaster
V259LRSKRVAPVLI4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
V259LRSKRLAPVMI1Arabidopsis thaliana
V271EITRRVHLEGI3Homo sapiens, Mus musculus, Rattus norvegicus
V271EVTRRVHLENI1Arabidopsis thaliana
V271EITRRVNLTGI1Drosophila melanogaster
V425YSFYNVHTQTP3Homo sapiens, Mus musculus, Rattus norvegicus
V425YSYYNVATQTS1Arabidopsis thaliana
V425YSFYNVSTKTP1Drosophila melanogaster
W120RSYQFWDTQPV3Homo sapiens, Mus musculus, Rattus norvegicus
W120KTHKFWETQPV1Arabidopsis thaliana
W120KKFAFWSTQPV1Drosophila melanogaster
Y117ASKRSYQFWDT3Homo sapiens, Mus musculus, Rattus norvegicus
Y117SEAKTHKFWET1Arabidopsis thaliana
Y117---KKFAFWST1Drosophila melanogaster
Y180LLNENYVEDDD4Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster
Y180LLKNNYVEDDE1Arabidopsis thaliana
Y281IFQAVYTAGVV3Homo sapiens, Mus musculus, Rattus norvegicus
Y281IWQAAYTAGVI1Arabidopsis thaliana
Y281IFQAAYTAGVV1Drosophila melanogaster
Y296VGTCRYWHRSL3Homo sapiens, Mus musculus, Rattus norvegicus
Y296ITTCQYWHRSL1Arabidopsis thaliana
Y296VATCRYWHRSL1Drosophila melanogaster
Y420SLKAAYSFYNV3Homo sapiens, Mus musculus, Rattus norvegicus
Y420TLKAAYSYYNV1Arabidopsis thaliana
Y420TVRAAYSFYNV1Drosophila melanogaster
Y423AAYSFYNVHTQ3Homo sapiens, Mus musculus, Rattus norvegicus
Y423AAYSYYNVATQ1Arabidopsis thaliana
Y423AAYSFYNVSTK1Drosophila melanogaster
Y479LQYYLYNWKCP3Homo sapiens, Mus musculus, Rattus norvegicus
Y479LHYYLYNYRLK1Arabidopsis thaliana
Y479LQYYLYNWRCP1Drosophila melanogaster


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