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 SDS
Gene summary
Basic gene Info.Gene symbolSDS
Gene nameserine dehydratase
CytomapUCSC genome browser: 12q24.13
Type of geneprotein-coding
DescriptionL-serine ammonia-lyaseL-serine deaminaseL-serine dehydrataseL-serine dehydratase/L-threonine deaminaseL-threonine dehydrataseTDH
Modification date20141207
dbXrefs MIM : 182128
Ensembl : ENSG00000135094
HPRD : 01633
Vega : OTTHUMG00000169554
ProteinUniProt: P20132
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SDS
BioGPS: 10993
PathwayNCI Pathway Interaction Database: SDS
Pathway Commons: SDS
ContextiHOP: SDS
ligand binding site mutation search in PubMed: SDS
UCL Cancer Institute: SDS
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006565L-serine catabolic process15689518
GO:0042866pyruvate biosynthetic process15689518

Ligand binding site mutations for SDS

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for SDS
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
(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 SDS from PDB

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


Phenotype information for SDS
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for SDS
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
NutraceuticalDB00114Pyridoxal PhosphateSmall molecule
Approved|nutraceuticalDB00133L-SerineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SDS go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of SDS
Multiple alignments for P20132 in multiple species
LBSAA sequence# speciesSpecies
A222TSVAKALGVNT2Mus musculus, Rattus norvegicus
A222TSVAKALGVKT1Homo sapiens
A222TSVAKALGVTT1Bos taurus
A269ILVEPACGAAL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
C303LVVIVCGGSNI4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F40QPSGSFKIRGI4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G168IVLSVGGGGLL2Mus musculus, Rattus norvegicus
G168IALSVGGGGLL1Homo sapiens
G168IVLAVGGGGLL1Bos taurus
G169VLSVGGGGLLC2Mus musculus, Rattus norvegicus
G169ALSVGGGGLLC1Homo sapiens
G169VLAVGGGGLLC1Bos taurus
G170LSVGGGGLLCG3Homo sapiens, Mus musculus, Rattus norvegicus
G170LAVGGGGLLCG1Bos taurus
G171SVGGGGLLCGV3Homo sapiens, Mus musculus, Rattus norvegicus
G171AVGGGGLLCGV1Bos taurus
G304VVIVCGGSNIS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G305VIVCGGSNISL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K41PSGSFKIRGIG4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
L172VGGGGLLCGVV4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
L223SVAKALGVNTV2Mus musculus, Rattus norvegicus
L223SVAKALGVKTV1Homo sapiens
L223SVAKALGVTTV1Bos taurus
N67---AGNAGMAA2Homo sapiens, Bos taurus
N67---AGNAGMAT1Mus musculus
N67PLTAGNAGMAT1Rattus norvegicus
S166GAIVLSVGGGG2Mus musculus, Rattus norvegicus
S166GAIALSVGGGG1Homo sapiens
S166GAIVLAVGGGG1Bos taurus
V167AIVLSVGGGGL2Mus musculus, Rattus norvegicus
V167AIALSVGGGGL1Homo sapiens
V167AIVLAVGGGGL1Bos taurus

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