Structure of PDB 6f6u Chain A Binding Site BS02

Receptor Information
>6f6u Chain A (length=328) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLK
TFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEA
VFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHH
LAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADL
KTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWT
DRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWET
WADLVHPDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDCV8
InChIInChI=1S/C21H30N2O5/c1-15-12-23(13-16(2)27-15)21(24)14-26-22-11-17-8-9-19(25-3)20(10-17)28-18-6-4-5-7-18/h8-11,15-16,18H,4-7,12-14H2,1-3H3/b22-11+/t15-,16+
InChIKeyJEXHQZPMUKFOIV-RULQDBOMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@@H]1CN(C[C@@H](O1)C)C(=O)CO/N=C/c2ccc(c(c2)OC3CCCC3)OC
OpenEye OEToolkits 2.0.6CC1CN(CC(O1)C)C(=O)CON=Cc2ccc(c(c2)OC3CCCC3)OC
CACTVS 3.385COc1ccc(/C=N/OCC(=O)N2C[C@H](C)O[C@H](C)C2)cc1OC3CCCC3
CACTVS 3.385COc1ccc(C=NOCC(=O)N2C[CH](C)O[CH](C)C2)cc1OC3CCCC3
FormulaC21 H30 N2 O5
Name2-[(~{E})-(3-cyclopentyloxy-4-methoxy-phenyl)methylideneamino]oxy-1-[(2~{R},6~{S})-2,6-dimethylmorpholin-4-yl]ethanone
ChEMBL
DrugBank
ZINC
PDB chain6f6u Chain A Residue 604 [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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PDB6f6u Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds.
Resolution1.828 Å
Binding residue
(original residue number in PDB)		Y325 S374 M439 T499 I502 F506 Q535 F538
Binding residue
(residue number reindexed from 1)		Y76 S125 M190 T250 I253 F257 Q286 F289
Annotation score1
Binding affinityMOAD: ic50=16uM
PDBbind-CN: -logKd/Ki=4.80,IC50=16uM
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:6f6u, PDBe:6f6u, PDBj:6f6u
PDBsum6f6u
PubMed29652483
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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