Structure of PDB 6fdc Chain A Binding Site BS03

Receptor Information
>6fdc Chain A (length=329) 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
TWADLVHPDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDDD5
InChIInChI=1S/C22H29F2N3O4/c23-22(24)31-20-6-5-16(13-21(20)30-18-3-1-2-4-18)19-7-8-27(25-19)15-17(28)14-26-9-11-29-12-10-26/h5-8,13,17-18,22,28H,1-4,9-12,14-15H2/t17-/m1/s1
InChIKeyFRVKKFLTBQINJK-QGZVFWFLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[CH](CN1CCOCC1)Cn2ccc(n2)c3ccc(OC(F)F)c(OC4CCCC4)c3
OpenEye OEToolkits 2.0.6c1cc(c(cc1c2ccn(n2)C[C@@H](CN3CCOCC3)O)OC4CCCC4)OC(F)F
CACTVS 3.385O[C@H](CN1CCOCC1)Cn2ccc(n2)c3ccc(OC(F)F)c(OC4CCCC4)c3
OpenEye OEToolkits 2.0.6c1cc(c(cc1c2ccn(n2)CC(CN3CCOCC3)O)OC4CCCC4)OC(F)F
FormulaC22 H29 F2 N3 O4
Name(2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol
ChEMBLCHEMBL5286787
DrugBank
ZINC
PDB chain6fdc Chain A Residue 606 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fdc Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		Y325 H326 N487 P488 Y495 W498 T499 I502 F506 P522 M523 Q535 F538
Binding residue
(residue number reindexed from 1)		Y77 H78 N239 P240 Y247 W250 T251 I254 F258 P274 M275 Q287 F290
Annotation score1
Binding affinityMOAD: ic50=2.3uM
PDBbind-CN: -logKd/Ki=5.64,IC50=2.3uM
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:6fdc, PDBe:6fdc, PDBj:6fdc
PDBsum6fdc
PubMed29652483
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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