Structure of PDB 2qyk Chain B Binding Site BS01

Receptor Information
>2qyk Chain B (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMNIPRFGVKTDQEELLAQELENLNKWGLNIFCVSDYAGGRSLTCIMYMI
FQERDLLKKFRIPVDTMVTYMLTLEDHYHADVAYHNSLHAADVLQSTHVL
LATPALDAVFTDLEILAALFAAAIHDVDHPGVSNQFLINTNSELALMYND
ESVLENHHLAVGFKLLQEDNCDIFQNLSKRQRQSLRKMVIDMVLATDMSK
HMTLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLRNMVHCADLSNPTKP
LELYRQWTDRIMAEFFQQGDRERERGMEISPMCDKHTASVEKSQVGFIDY
IVHPLWETWADLVHPDAQEILDTLEDNRDWYYSAI
Ligand information
Ligand IDNPV
InChIInChI=1S/C21H13N3O4/c25-21(26)14-8-6-13(7-9-14)18-12-16-4-2-10-22-19(16)20(23-18)15-3-1-5-17(11-15)24(27)28/h1-12H,(H,25,26)
InChIKeyQTNUWEKKZHSUQO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)c1ccc(cc1)c2cc3cccnc3c(n2)c4cccc(c4)[N+]([O-])=O
ACDLabs 10.04[O-][N+](=O)c1cccc(c1)c3nc(cc2c3nccc2)c4ccc(C(=O)O)cc4
OpenEye OEToolkits 1.5.0c1cc(cc(c1)[N+](=O)[O-])c2c3c(cccn3)cc(n2)c4ccc(cc4)C(=O)O
FormulaC21 H13 N3 O4
Name4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid
ChEMBLCHEMBL74078
DrugBankDB08299
ZINC
PDB chain2qyk Chain B Residue 3 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2qyk Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y371 M485 N533 I548 F552 M569 S580 Q581 F584
Binding residue
(residue number reindexed from 1)		Y84 M198 N246 I261 F265 M282 S293 Q294 F297
Annotation score1
Binding affinityMOAD: ic50=3.3uM
BindingDB: IC50=3300nM,EC50=20nM
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:2qyk, PDBe:2qyk, PDBj:2qyk
PDBsum2qyk
PubMed17727341
UniProtP27815|PDE4A_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4A (Gene Name=PDE4A)

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