Structure of PDB 3iad Chain B Binding Site BS01

Receptor Information
>3iad Chain B (length=338) 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
VHPDAQDILDTLEDNREWYQSTIPQNQVSEFISNTFLD
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 B 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)		M439 I502 F506 S534 Q535 F538 F599 T603
Binding residue
(residue number reindexed from 1)		M186 I249 F253 S281 Q282 F285 F331 T335
Annotation score1
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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