Structure of PDB 2qyl Chain A Binding Site BS03

Receptor Information
>2qyl Chain A (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIF
QERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLL
STPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDE
SVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKH
MSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSL
ELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYI
VHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIP
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 chain2qyl Chain A 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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PDB2qyl Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		Y233 M347 N395 I410 F414 Q443 F446
Binding residue
(residue number reindexed from 1)		Y83 M197 N245 I260 F264 Q293 F296
Annotation score1
Binding affinityMOAD: ic50=0.65uM
PDBbind-CN: -logKd/Ki=6.19,IC50=0.65uM
BindingDB: IC50=650nM
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
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Biological Process
External links
PDB RCSB:2qyl, PDBe:2qyl, PDBj:2qyl
PDBsum2qyl
PubMed17727341
UniProtQ07343|PDE4B_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4B (Gene Name=PDE4B)

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