Structure of PDB 6fw3 Chain B Binding Site BS02

Receptor Information
>6fw3 Chain B (length=323) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIP
VDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDL
EILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGF
KLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVE
TKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIME
EFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLV
HPDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDE8H
InChIInChI=1S/C27H32N4O6/c1-36-21-8-7-17(15-22(21)37-2)26-19-5-3-4-6-20(19)27(35)31(28-26)18-11-13-29(14-12-18)25(34)16-30-23(32)9-10-24(30)33/h3-4,7-8,15,18-20H,5-6,9-14,16H2,1-2H3/t19-,20+/m0/s1
InChIKeyBLRZNXZBGGTDMQ-VQTJNVASSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(cc1OC)C2=NN(C3CCN(CC3)C(=O)CN4C(=O)CCC4=O)C(=O)[CH]5CC=CC[CH]25
CACTVS 3.385COc1ccc(cc1OC)C2=NN(C3CCN(CC3)C(=O)CN4C(=O)CCC4=O)C(=O)[C@@H]5CC=CC[C@H]25
OpenEye OEToolkits 2.0.6COc1ccc(cc1OC)C2=NN(C(=O)[C@H]3[C@@H]2CC=CC3)C4CCN(CC4)C(=O)CN5C(=O)CCC5=O
OpenEye OEToolkits 2.0.6COc1ccc(cc1OC)C2=NN(C(=O)C3C2CC=CC3)C4CCN(CC4)C(=O)CN5C(=O)CCC5=O
FormulaC27 H32 N4 O6
Name1-(2-{4-[(4aS,8aR)-4-(3,4-dimethoxyphenyl)-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)pyrrolidine-2,5-dione
ChEMBLCHEMBL4566742
DrugBank
ZINC
PDB chain6fw3 Chain B Residue 517 [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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PDB6fw3 hPDE4D2 structure with inhibitor NPD-007
Resolution1.78 Å
Binding residue
(original residue number in PDB)		M273 I336 M357 Q369 F372
Binding residue
(residue number reindexed from 1)		M185 I248 M269 Q281 F284
Annotation score1
Binding affinityBindingDB: Ki=0.061660nM
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:6fw3, PDBe:6fw3, PDBj:6fw3
PDBsum6fw3
PubMed
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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