Structure of PDB 2qyn Chain B Binding Site BS01

Receptor Information
>2qyn Chain B (length=325) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKI
PVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTD
LEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVG
FKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMV
ETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIM
EEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADL
VHPDAQDILDTLEDNREWYQSTIPQ
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 chain2qyn Chain B Residue 1 [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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PDB2qyn Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		Y159 H160 M273 N321 I336 F340 M357 Q369 F372
Binding residue
(residue number reindexed from 1)		Y72 H73 M186 N234 I249 F253 M270 Q282 F285
Annotation score1
Binding affinityMOAD: ic50=0.57uM
BindingDB: IC50=1nM
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:2qyn, PDBe:2qyn, PDBj:2qyn
PDBsum2qyn
PubMed17727341
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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