Structure of PDB 6fdi Chain A Binding Site BS02

Receptor Information
>6fdi Chain A (length=330) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDL
LKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPAL
EAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLEN
HHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLA
DLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQ
WTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLW
ETWADLVHPDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDD5T
InChIInChI=1S/C30H38N4O6/c1-30(2)16-25(35)33(26(36)17-30)18-27(37)32-13-11-20(12-14-32)34-29(38)22-8-6-5-7-21(22)28(31-34)19-9-10-23(39-3)24(15-19)40-4/h5-6,9-10,15,20-22H,7-8,11-14,16-18H2,1-4H3/t21-,22+/m0/s1
InChIKeyDZMHUZHTZIODAZ-FCHUYYIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(cc1OC)C2=NN(C3CCN(CC3)C(=O)CN4C(=O)CC(C)(C)CC4=O)C(=O)[CH]5CC=CC[CH]25
OpenEye OEToolkits 2.0.6CC1(CC(=O)N(C(=O)C1)CC(=O)N2CCC(CC2)N3C(=O)C4CC=CCC4C(=N3)c5ccc(c(c5)OC)OC)C
OpenEye OEToolkits 2.0.6CC1(CC(=O)N(C(=O)C1)CC(=O)N2CCC(CC2)N3C(=O)[C@@H]4CC=CC[C@@H]4C(=N3)c5ccc(c(c5)OC)OC)C
CACTVS 3.385COc1ccc(cc1OC)C2=NN(C3CCN(CC3)C(=O)CN4C(=O)CC(C)(C)CC4=O)C(=O)[C@@H]5CC=CC[C@H]25
FormulaC30 H38 N4 O6
Name1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione;
NPD-226
ChEMBLCHEMBL4441748
DrugBank
ZINC
PDB chain6fdi Chain A Residue 514 [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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PDB6fdi hPDE4D2 structure with inhibitor NPD-226
Resolution1.9 Å
Binding residue
(original residue number in PDB)		M273 I336 M357 Q369 F372
Binding residue
(residue number reindexed from 1)		M192 I255 M276 Q288 F291
Annotation score1
Binding affinityBindingDB: Ki=0.123027nM
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:6fdi, PDBe:6fdi, PDBj:6fdi
PDBsum6fdi
PubMed
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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