Structure of PDB 6f8x Chain A Binding Site BS03

Receptor Information
>6f8x 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 IDD08
InChIInChI=1S/C21H30N2O6/c1-27-19-7-6-15(12-20(19)28-16-4-2-3-5-16)18-13-17(29-22-18)14-21(26)23(8-10-24)9-11-25/h6-7,12,16-17,24-25H,2-5,8-11,13-14H2,1H3/t17-/m1/s1
InChIKeyVUQABPCUWUTWEU-QGZVFWFLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COc1ccc(cc1OC2CCCC2)C3=NO[C@H](C3)CC(=O)N(CCO)CCO
CACTVS 3.385COc1ccc(cc1OC2CCCC2)C3=NO[C@@H](CC(=O)N(CCO)CCO)C3
CACTVS 3.385COc1ccc(cc1OC2CCCC2)C3=NO[CH](CC(=O)N(CCO)CCO)C3
OpenEye OEToolkits 2.0.6COc1ccc(cc1OC2CCCC2)C3=NOC(C3)CC(=O)N(CCO)CCO
FormulaC21 H30 N2 O6
Name2-[(5~{R})-3-(3-cyclopentyloxy-4-methoxy-phenyl)-4,5-dihydro-1,2-oxazol-5-yl]-~{N},~{N}-bis(2-hydroxyethyl)ethanamide
ChEMBL
DrugBank
ZINC
PDB chain6f8x Chain A Residue 605 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6f8x Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		Y325 S374 N375 M439 N487 I502 M503 F506 M523 S534 Q535 F538
Binding residue
(residue number reindexed from 1)		Y70 S119 N120 M184 N232 I247 M248 F251 M268 S279 Q280 F283
Annotation score1
Binding affinityMOAD: ic50=17uM
PDBbind-CN: -logKd/Ki=4.77,IC50=17uM
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:6f8x, PDBe:6f8x, PDBj:6f8x
PDBsum6f8x
PubMed29652483
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

[Back to BioLiP]