mutLBSgeneDB |
Gene summary for PDE1B |
Gene summary |
Basic gene Info. | Gene symbol | PDE1B |
Gene name | phosphodiesterase 1B, calmodulin-dependent | |
Synonyms | PDE1B1|PDES1B | |
Cytomap | UCSC genome browser: 12q13 | |
Type of gene | protein-coding | |
RefGenes | NM_000924.3, NM_001165975.2,NM_001288768.1,NM_001288769.1, | |
Description | 63 kDa Cam-PDEcalcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1Bcalcium/calmodulin-stimulated cyclic nucleotide phosphodiesterasecalmodulin-stimulated phosphodiesterase PDE1B1cam-PDE 1Bpresumed 63kDa form of the type 1 cyclic n | |
Modification date | 20141207 | |
dbXrefs | MIM : 171891 | |
HGNC : HGNC | ||
Ensembl : ENSG00000123360 | ||
HPRD : 01388 | ||
Vega : OTTHUMG00000169844 | ||
Protein | UniProt: Q01064 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PDE1B | |
BioGPS: 5153 | ||
Pathway | NCI Pathway Interaction Database: PDE1B | |
KEGG: PDE1B | ||
REACTOME: PDE1B | ||
Pathway Commons: PDE1B | ||
Context | iHOP: PDE1B | |
ligand binding site mutation search in PubMed: PDE1B | ||
UCL Cancer Institute: PDE1B | ||
Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO Term | PubMed ID | GO:0006198 | cAMP catabolic process | 14687666 | GO:0036006 | cellular response to macrophage colony-stimulating factor stimulus | 14687666 | GO:0046069 | cGMP catabolic process | 14687666 | GO:0097011 | cellular response to granulocyte macrophage colony-stimulating factor stimulus | 14687666 |
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Ligand binding site mutations for PDE1B |
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 |
LBS | AAchange of nsSNV | Cancer type | # samples | H227 | A228S | LUSC | 1 | H263 | H263Y | SKCM | 1 |
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 PDE1B |
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. |
LBS | AAchange of nsSNV | Relative stability change | H227 | A228S | -0.75719955 | H263 | H263Y | -0.024121873 |
(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 PDE1B from PDB |
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Differential gene expression and gene-gene network for PDE1B |
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) |
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Phenotype information for PDE1B |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0023186 | Learning Disorders | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for PDE1B |
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 status | DrugBank ID | Name | Type | Drug structure |
Approved | DB00622 | Nicardipine | Small molecule | |
Approved|investigational | DB01023 | Felodipine | Small molecule | |
Approved|withdrawn | DB01244 | Bepridil | Small molecule | |
Experimental | DB04530 | S,S-(2-Hydroxyethyl)Thiocysteine | Small molecule |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of PDE1B go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 1taz | A | H227 H263 |
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Conservation information for LBS of PDE1B |
Multiple alignments for Q01064 in multiple species |
LBS | AA sequence | # species | Species | D264 | AAAIHDYEHTG | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | D370 | LLHAADISHPT | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | H227 | YHNQIHAADVT | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | H263 | FAAAIHDYEHT | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus |
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