Structure of PDB 3g4k Chain B Binding Site BS02

Receptor Information
>3g4k Chain B (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFK
IPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFT
DLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAV
GFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTM
VETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRI
MEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWAD
LVHPDAQDILDTLEDNREWYQSTIPQ
Ligand information
Ligand IDROL
InChIInChI=1S/C16H21NO3/c1-19-14-7-6-11(12-9-16(18)17-10-12)8-15(14)20-13-4-2-3-5-13/h6-8,12-13H,2-5,9-10H2,1H3,(H,17,18)/t12-/m0/s1
InChIKeyHJORMJIFDVBMOB-LBPRGKRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1ccc(cc1OC2CCCC2)[C@@H]3CNC(=O)C3
OpenEye OEToolkits 1.5.0COc1ccc(cc1OC2CCCC2)C3CC(=O)NC3
OpenEye OEToolkits 1.5.0COc1ccc(cc1OC2CCCC2)[C@H]3CC(=O)NC3
CACTVS 3.341COc1ccc(cc1OC2CCCC2)[CH]3CNC(=O)C3
ACDLabs 10.04O=C3NCC(c2cc(OC1CCCC1)c(OC)cc2)C3
FormulaC16 H21 N O3
NameROLIPRAM;
(4R)-[3-(CYCLOPENTYLOXY)-4-METHOXYPHENYL]-2-PYRROLIDINONE
ChEMBLCHEMBL430893
DrugBankDB04149
ZINCZINC000000004982
PDB chain3g4k Chain B Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3g4k Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		Y325 H326 T499 I502 M523 S534 Q535 F538
Binding residue
(residue number reindexed from 1)		Y73 H74 T247 I250 M271 S282 Q283 F286
Annotation score1
Binding affinityMOAD: ic50=288nM
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:3g4k, PDBe:3g4k, PDBj:3g4k
PDBsum3g4k
PubMed20037581
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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