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 PDE3B
Gene summary
Basic gene Info.Gene symbolPDE3B
Gene namephosphodiesterase 3B, cGMP-inhibited
SynonymsHcGIP1|cGIPDE1
CytomapUCSC genome browser: 11p15.1
Type of geneprotein-coding
RefGenesNM_000922.3,
DescriptionCGI-PDE BCGIP1cGMP-inhibited 3',5'-cyclic phosphodiesterase Bcyclic GMP-inhibited phosphodiesterase Bcyclic nucleotide phosphodiesterase
Modification date20141207
dbXrefs MIM : 602047
HGNC : HGNC
Ensembl : ENSG00000152270
HPRD : 03626
Vega : OTTHUMG00000165898
ProteinUniProt: Q13370
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE3B
BioGPS: 5140
PathwayNCI Pathway Interaction Database: PDE3B
KEGG: PDE3B
REACTOME: PDE3B
Pathway Commons: PDE3B
ContextiHOP: PDE3B
ligand binding site mutation search in PubMed: PDE3B
UCL Cancer Institute: PDE3B
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


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Ligand binding site mutations for PDE3B
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
I995H994NLUAD1
H821H821NLUAD1
N957N957ILUAD1
I955I955TSTAD1
H737,H741R739CUCEC1
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 PDE3B
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
N957N957I0.071943246
I955I955T-1.4133055
I995H994N-0.90017469
H737R739C-0.6140769
H741R739C-0.6140769
H821H821N-0.55165402
(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 PDE3B from PDB

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Differential gene expression and gene-gene network for PDE3B
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 PDE3B and the right PPI network was created from samples without mutations in the LBS of PDE3B. 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 PDE3B
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0032460Polycystic Ovary Syndrome1Biomarker

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

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Pharmacological information for PDE3B
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
ExperimentalDB01640(5r)-6-(4-{[2-(3-Iodobenzyl)-3-Oxocyclohex-1-En-1-Yl]Amino}Phenyl)-5-Methyl-4,5-Dihydropyridazin-3(2h)-OneSmall molecule
ExperimentalDB01970Hg9a-9, Nonanoyl-N-HydroxyethylglucamideSmall molecule
ExperimentalDB079543-isobutyl-1-methyl-7H-xanthineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PDE3B go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojLH737 I955
MGMAGNESIUM(2+)1so2AH741 H821
MGMAGNESIUM(2+)1so2BH741 H821
MGMAGNESIUM(2+)1so2CH741 H821
MGMAGNESIUM(2+)1so2DH741 H821
MGMAGNESIUM(2+)1sojAH741 H821
MGMAGNESIUM(2+)1sojBH741 H821
MGMAGNESIUM(2+)1sojCH741 H821
MGMAGNESIUM(2+)1sojDH741 H821
MGMAGNESIUM(2+)1sojEH741 H821
MGMAGNESIUM(2+)1sojFH741 H821
MGMAGNESIUM(2+)1sojGH741 H821
MGMAGNESIUM(2+)1sojHH741 H821
MGMAGNESIUM(2+)1sojIH741 H821
MGMAGNESIUM(2+)1sojJH741 H821
MGMAGNESIUM(2+)1sojKH741 H821
MGMAGNESIUM(2+)1sojLH741 H821
MGMAGNESIUM(2+)1so2DH821
666(5R)-6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE1so2CI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojAI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojBI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojCI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojDI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojEI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojFI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojGI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojHI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojII955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojJI955
IBM3-ISOBUTYL-1-METHYL-9H-XANTHINE1sojKI955
666(5R)-6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE1so2AI995
666(5R)-6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE1so2BI995
HG9NONANOYL-N-HYDROXYETHYLGLUCAMIDE1so2AN957
HG9NONANOYL-N-HYDROXYETHYLGLUCAMIDE1so2BN957


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Conservation information for LBS of PDE3B
Multiple alignments for Q13370 in multiple species
LBSAA sequence# speciesSpecies
A985SSPQLAKLQES3Homo sapiens, Mus musculus, Rattus norvegicus
D822AAAMHDYDHPG3Homo sapiens, Mus musculus, Rattus norvegicus
D937CIKLADINGPA3Homo sapiens, Mus musculus, Rattus norvegicus
E953HLRWTEGIVNE2Mus musculus, Rattus norvegicus
E953HLKWTEGIVNE1Homo sapiens
F959GIVNEFYEQGD3Homo sapiens, Mus musculus, Rattus norvegicus
F976LPISPFMDRSS3Homo sapiens, Mus musculus, Rattus norvegicus
F991KLQESFITHIV3Homo sapiens, Mus musculus, Rattus norvegicus
G940LADINGPAKDR2Mus musculus, Rattus norvegicus
G940LADINGPAKVR1Homo sapiens
H737RDIPYHNRVHA2Mus musculus, Rattus norvegicus
H737RDIPYHNRIHA1Homo sapiens
H741YHNRVHATDVL2Mus musculus, Rattus norvegicus
H741YHNRIHATDVL1Homo sapiens
H821VAAAMHDYDHP3Homo sapiens, Mus musculus, Rattus norvegicus
H948KDRDLHLRWTE2Mus musculus, Rattus norvegicus
H948KVRDLHLKWTE1Homo sapiens
I1071TENHKIWKEII2Mus musculus, Rattus norvegicus
I1071TENHKIWKEIV1Homo sapiens
I938IKLADINGPAK3Homo sapiens, Mus musculus, Rattus norvegicus
I955RWTEGIVNEFY2Mus musculus, Rattus norvegicus
I955KWTEGIVNEFY1Homo sapiens
I995SFITHIVGPLC3Homo sapiens, Mus musculus, Rattus norvegicus
K1070LTENHKIWKEI3Homo sapiens, Mus musculus, Rattus norvegicus
K9-ERDAKAMRSL1Homo sapiens
K9RERDAPAMRSP1Mus musculus
K9RERDTPAMRSP1Rattus norvegicus
L895ILATDLKKHFD3Homo sapiens, Mus musculus, Rattus norvegicus
L984RSSPQLAKLQE3Homo sapiens, Mus musculus, Rattus norvegicus
L987PQLAKLQESFI3Homo sapiens, Mus musculus, Rattus norvegicus
N957TEGIVNEFYEQ3Homo sapiens, Mus musculus, Rattus norvegicus
P941ADINGPAKDRD2Mus musculus, Rattus norvegicus
P941ADINGPAKVRD1Homo sapiens
Q988QLAKLQESFIT3Homo sapiens, Mus musculus, Rattus norvegicus
R979SPFMDRSSPQL3Homo sapiens, Mus musculus, Rattus norvegicus
S990AKLQESFITHI3Homo sapiens, Mus musculus, Rattus norvegicus
T829DHPGRTNAFLV3Homo sapiens, Mus musculus, Rattus norvegicus
T952LHLRWTEGIVN2Mus musculus, Rattus norvegicus
T952LHLKWTEGIVN1Homo sapiens
V956WTEGIVNEFYE3Homo sapiens, Mus musculus, Rattus norvegicus
W951DLHLRWTEGIV2Mus musculus, Rattus norvegicus
W951DLHLKWTEGIV1Homo sapiens
Y736YRDIPYHNRVH2Mus musculus, Rattus norvegicus
Y736YRDIPYHNRIH1Homo sapiens


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