Structure of PDB 5wh5 Chain B Binding Site BS01

Receptor Information
>5wh5 Chain B (length=325) 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
VHPDAQDILDTLEDNREWYQSTIPQ
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 B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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 M273 N321 Y329 W332 T333 I336 M357 S368 Q369 F372
Binding residue
(residue number reindexed from 1)		Y72 M186 N234 Y242 W245 T246 I249 M270 S281 Q282 F285
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:5wh5, PDBe:5wh5, PDBj:5wh5
PDBsum5wh5
PubMed29975048
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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