Structure of PDB 3iad Chain A Binding Site BS01

Receptor Information
>3iad Chain A (length=340) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLL
KTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALE
AVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENH
HLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLAD
LKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQW
TDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWE
TWADLVHPDAQDILDTLEDNREWYQSTNQVSEFISNTFLD
Ligand information
Ligand ID15X
InChIInChI=1S/C21H18FN3O4/c1-29-18-10-7-15(11-13-5-8-16(9-6-13)24-21(23)26)20(22)19(18)14-3-2-4-17(12-14)25(27)28/h2-10,12H,11H2,1H3,(H3,23,24,26)
InChIKeyANIKIUAKBPWSRA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COc1ccc(Cc2ccc(NC(N)=O)cc2)c(F)c1c3cccc(c3)[N](=O)=O
ACDLabs 11.02O=N(=O)c3cccc(c1c(F)c(ccc1OC)Cc2ccc(NC(=O)N)cc2)c3
OpenEye OEToolkits 1.7.0COc1ccc(c(c1c2cccc(c2)N(=O)=O)F)Cc3ccc(cc3)NC(=O)N
FormulaC21 H18 F N3 O4
Name1-{4-[(2-fluoro-6-methoxy-3'-nitrobiphenyl-3-yl)methyl]phenyl}urea
ChEMBLCHEMBL1229663
DrugBank
ZINCZINC000044667950
PDB chain3iad Chain A Residue 901 [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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PDB3iad Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		S374 F506 S534 Q535 F538 F599
Binding residue
(residue number reindexed from 1)		S126 F258 S286 Q287 F290 F333
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.00,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:3iad, PDBe:3iad, PDBj:3iad
PDBsum3iad
PubMed20037581
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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