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 SMS
Gene summary
Basic gene Info.Gene symbolSMS
Gene namespermine synthase
SynonymsMRSR|SPMSY|SRS|SpS
CytomapUCSC genome browser: Xp22.1
Type of geneprotein-coding
RefGenesNM_001258423.1,
NM_004595.4,
Descriptionspermidine aminopropyltransferase
Modification date20141219
dbXrefs MIM : 300105
HGNC : HGNC
Ensembl : ENSG00000102172
HPRD : 02115
Vega : OTTHUMG00000021239
ProteinUniProt: P52788
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMS
BioGPS: 6611
PathwayNCI Pathway Interaction Database: SMS
KEGG: SMS
REACTOME: SMS
Pathway Commons: SMS
ContextiHOP: SMS
ligand binding site mutation search in PubMed: SMS
UCL Cancer Institute: SMS
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 SMS

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
D167D167GCOAD1
T126D128EHNSC1
D276D276YKIRC1
D167G166VLUSC1
P125P125SSKCM1
W355V356ASTAD1
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 SMS
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
W355V356A-1.3222931
D167D167G-1.1644355
P125P125S-1.005705
D276D276Y-0.66881799
D167G166V-0.63299207
T126D128E-0.1676308
(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 SMS from PDB

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Differential gene expression and gene-gene network for SMS
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 SMS and the right PPI network was created from samples without mutations in the LBS of SMS. 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 SMS
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0796160Snyder Robinson syndrome8Biomarker, GeneticVariation

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

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Pharmacological information for SMS
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|nutraceuticalDB00127SpermineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SMS go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
SPMSPERMINE3c6mBD167 D276 W355
SPMSPERMINE3c6mCD167 D276 W355
MTA5'-DEOXY-5'-METHYLTHIOADENOSINE3c6mAD276
MTA5'-DEOXY-5'-METHYLTHIOADENOSINE3c6mBD276
MTA5'-DEOXY-5'-METHYLTHIOADENOSINE3c6mCD276
MTA5'-DEOXY-5'-METHYLTHIOADENOSINE3c6mDD276
SPMSPERMINE3c6mAP125 D167 D276 W355
SPMSPERMINE3c6mDT126 D167 D276 W355


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Conservation information for LBS of SMS
Multiple alignments for P52788 in multiple species
LBSAA sequence# speciesSpecies
C256VLIEDCIPVLK4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
D167LILSGDVNLAE4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
D201ILGGGDGGILC4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
D222TMVEIDQMVID4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
D255QVLIEDCIPVL4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
D276DYVINDLTAVP4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
E220MVTMVEIDQMV4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
E353VPSYLELWVFY4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
G198DVLILGGGDGG4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
G199VLILGGGDGGI4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
G200LILGGGDGGIL4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
I221VTMVEIDQMVI4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
I282LTAVPISTSPE4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
L162QFGNILILSGD4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
L164GNILILSGDVN4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
L277YVINDLTAVPI4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
N169LSGDVNLAESD4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
P125IDRYWPTADGR4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
Q148EDSPYQNIKIL4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
Q315GKYFTQGNCVN4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
T126DRYWPTADGRL4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
T278VINDLTAVPIS4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
V168ILSGDVNLAES4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
V219KMVTMVEIDQM4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
V225EIDQMVIDGCK4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
W124AIDRYWPTADG4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
W355SYLELWVFYTV4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
Y134GRLVEYDIDEV3Homo sapiens, Mus musculus, Mus musculus
Y134GRLVEYDIDKV1Bos taurus
Y177ESDLAYTRAIM4Homo sapiens, Mus musculus, Mus musculus, Bos taurus
Y351VCVPSYLELWV4Homo sapiens, Mus musculus, Mus musculus, Bos taurus


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