Structure of PDB 6f8u Chain A Binding Site BS03

Receptor Information
>6f8u Chain A (length=322) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPV
DTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLE
ILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFK
LLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVET
KKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEE
FFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVH
PDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDCZQ
InChIInChI=1S/C21H28F2N2O5/c1-14-11-25(12-15(2)28-14)20(26)13-27-24-10-16-7-8-18(30-21(22)23)19(9-16)29-17-5-3-4-6-17/h7-10,14-15,17,21H,3-6,11-13H2,1-2H3/b24-10+/t14-,15-/m1/s1
InChIKeyYRGXPDDUADZCCU-BAMVQPFASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1CN(CC(O1)C)C(=O)CON=Cc2ccc(c(c2)OC3CCCC3)OC(F)F
CACTVS 3.385C[CH]1CN(C[CH](C)O1)C(=O)CON=Cc2ccc(OC(F)F)c(OC3CCCC3)c2
OpenEye OEToolkits 2.0.6C[C@@H]1CN(C[C@H](O1)C)C(=O)CO/N=C/c2ccc(c(c2)OC3CCCC3)OC(F)F
CACTVS 3.385C[C@@H]1CN(C[C@@H](C)O1)C(=O)CO/N=C/c2ccc(OC(F)F)c(OC3CCCC3)c2
FormulaC21 H28 F2 N2 O5
Name2-[(~{E})-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]methylideneamino]oxy-1-[(2~{R},6~{R})-2,6-dimethylmorpholin-4-yl]ethanone
ChEMBL
DrugBank
ZINCZINC000473136172
PDB chain6f8u Chain A Residue 606 [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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PDB6f8u Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		S374 N487 Y495 W498 T499 I502 F506 Q509 M523 S534 Q535 F538
Binding residue
(residue number reindexed from 1)		S119 N232 Y240 W243 T244 I247 F251 Q254 M268 S279 Q280 F283
Annotation score1
Binding affinityMOAD: ic50=0.8uM
PDBbind-CN: -logKd/Ki=6.10,IC50=0.8uM
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
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Biological Process
External links
PDB RCSB:6f8u, PDBe:6f8u, PDBj:6f8u
PDBsum6f8u
PubMed29652483
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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