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 PDLIM1
Gene summary
Basic gene Info.Gene symbolPDLIM1
Gene namePDZ and LIM domain 1
CytomapUCSC genome browser: 10q23.1
Type of geneprotein-coding
DescriptionLIM domain protein CLP-36PDZ and LIM domain protein 1carboxyl terminal LIM domain protein 1elfinepididymis secretory protein Li 112
Modification date20141207
dbXrefs MIM : 605900
Ensembl : ENSG00000107438
HPRD : 09326
Vega : OTTHUMG00000018810
ProteinUniProt: O00151
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDLIM1
BioGPS: 9124
PathwayNCI Pathway Interaction Database: PDLIM1
Pathway Commons: PDLIM1
ContextiHOP: PDLIM1
ligand binding site mutation search in PubMed: PDLIM1
UCL Cancer Institute: PDLIM1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for PDLIM1

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 PDLIM1
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 PDLIM1 from PDB

Differential gene expression and gene-gene network for PDLIM1
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 PDLIM1 and the right PPI network was created from samples without mutations in the LBS of PDLIM1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PDLIM1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for PDLIM1
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PDLIM1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of PDLIM1
Multiple alignments for O00151 in multiple species
LBSAA sequence# speciesSpecies
C260QKLPMCDKCGT2Homo sapiens, Bos taurus
C260QKLPICDKCGT2Mus musculus, Rattus norvegicus
C263PMCDKCGTGIV2Homo sapiens, Bos taurus
C263PICDKCGTGIV2Mus musculus, Rattus norvegicus
C283HRHPECYVCTD4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
C286PECYVCTDCGT2Homo sapiens, Bos taurus
C286PECYVCTDCGI2Mus musculus, Rattus norvegicus
C289YVCTDCGTNLK2Homo sapiens, Bos taurus
C289YVCTDCGINLK2Mus musculus, Rattus norvegicus
C307EDQIYCEKHAR3Homo sapiens, Mus musculus, Bos taurus
C307GDQIYCEKHAR1Rattus norvegicus
H280RDHHRHPECYV2Mus musculus, Rattus norvegicus
H280RDRHRHPECYV1Homo sapiens
H280RERHRHPECYV1Bos taurus
H310IYCEKHARERV4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus

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