Structure of PDB 1y2b Chain B Binding Site BS02

Receptor Information
>1y2b Chain B (length=322) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTF
KIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVF
TDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLA
VGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKT
MVETKKVVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEE
FFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVH
PDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDDEE
InChIInChI=1S/C8H12N2O2/c1-4-12-8(11)7-5(2)9-10-6(7)3/h4H2,1-3H3,(H,9,10)
InChIKeyBCKARVLFIJPHQU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCOC(=O)c1c([nH]nc1C)C
CACTVS 3.341CCOC(=O)c1c(C)[nH]nc1C
ACDLabs 10.04O=C(OCC)c1c(nnc1C)C
FormulaC8 H12 N2 O2
Name3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER
ChEMBLCHEMBL506972
DrugBankDB04271
ZINCZINC000000109930
PDB chain1y2b Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1y2b A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design
Resolution1.4 Å
Binding residue
(original residue number in PDB)		Y159 T333 I336 Q369 F372
Binding residue
(residue number reindexed from 1)		Y74 T244 I247 Q280 F283
Annotation score1
Binding affinityMOAD: ic50=82uM
BindingDB: IC50=82000nM
Enzymatic activity
Enzyme Commision number 3.1.4.53: 3',5'-cyclic-AMP phosphodiesterase.
Gene Ontology
Molecular Function
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0008081 phosphoric diester hydrolase activity
Biological Process
GO:0007165 signal transduction

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1y2b, PDBe:1y2b, PDBj:1y2b
PDBsum1y2b
PubMed15685167
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

[Back to BioLiP]