Structure of PDB 5wh5 Chain A Binding Site BS01

Receptor Information
>5wh5 Chain A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTF
KIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVF
TDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLA
VGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKT
MVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDR
IMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWA
DLVHPDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDR91
InChIInChI=1S/C16H20F2O4/c1-10(2)7-13(19)11-3-4-14(22-16(17)18)15(8-11)21-12-5-6-20-9-12/h3-4,8,10,12,16H,5-7,9H2,1-2H3/t12-/m1/s1
InChIKeyIXURVUHDDXFYDR-GFCCVEGCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)Oc2c(OC1CCOC1)cc(cc2)C(=O)CC(C)C
OpenEye OEToolkits 2.0.6CC(C)CC(=O)c1ccc(c(c1)OC2CCOC2)OC(F)F
CACTVS 3.385CC(C)CC(=O)c1ccc(OC(F)F)c(O[CH]2CCOC2)c1
OpenEye OEToolkits 2.0.6CC(C)CC(=O)c1ccc(c(c1)O[C@@H]2CCOC2)OC(F)F
CACTVS 3.385CC(C)CC(=O)c1ccc(OC(F)F)c(O[C@@H]2CCOC2)c1
FormulaC16 H20 F2 O4
Name1-[4-(difluoromethoxy)-3-{[(3R)-oxolan-3-yl]oxy}phenyl]-3-methylbutan-1-one
ChEMBL
DrugBank
ZINCZINC000040864221
PDB chain5wh5 Chain A Residue 501 [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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PDB5wh5 Identification of a PDE4-Specific Pocket for the Design of Selective Inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Y159 N321 Y329 W332 T333 I336 M357 S368 Q369 F372
Binding residue
(residue number reindexed from 1)		Y74 N236 Y244 W247 T248 I251 M272 S283 Q284 F287
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.19,IC50=65nM
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:5wh5, PDBe:5wh5, PDBj:5wh5
PDBsum5wh5
PubMed29975048
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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