Structure of PDB 6ibf Chain D Binding Site BS02

Receptor Information
>6ibf Chain D (length=324) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKI
PVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTD
LEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVG
FKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMV
ETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIM
EEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADL
VHPDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand ID4I7
InChIInChI=1S/C34H32F3N5O3S/c1-44-28-11-10-21(18-29(28)45-19-22-6-2-5-9-26(22)34(35,36)37)30-24-7-3-4-8-25(24)33(43)42(40-30)23-12-15-41(16-13-23)32-31-27(14-17-46-31)38-20-39-32/h2-6,9-11,14,17-18,20,23-25H,7-8,12-13,15-16,19H2,1H3/t24-,25+/m0/s1
InChIKeyBVADHKPPTNFKBH-LOSJGSFVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(cc1OCc2ccccc2C(F)(F)F)C3=NN(C4CCN(CC4)c5ncnc6ccsc56)C(=O)[CH]7CC=CC[CH]37
OpenEye OEToolkits 2.0.6COc1ccc(cc1OCc2ccccc2C(F)(F)F)C3=NN(C(=O)C4C3CC=CC4)C5CCN(CC5)c6c7c(ccs7)ncn6
OpenEye OEToolkits 2.0.6COc1ccc(cc1OCc2ccccc2C(F)(F)F)C3=NN(C(=O)[C@H]4[C@@H]3CC=CC4)C5CCN(CC5)c6c7c(ccs7)ncn6
CACTVS 3.385COc1ccc(cc1OCc2ccccc2C(F)(F)F)C3=NN(C4CCN(CC4)c5ncnc6ccsc56)C(=O)[C@@H]7CC=CC[C@H]37
FormulaC34 H32 F3 N5 O3 S
Name(4~{a}~{S},8~{a}~{R})-4-[4-methoxy-3-[[2-(trifluoromethyl)phenyl]methoxy]phenyl]-2-(1-thieno[3,2-d]pyrimidin-4-ylpiperidin-4-yl)-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one
ChEMBL
DrugBank
ZINC
PDB chain6ibf Chain D Residue 520 [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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PDB6ibf hPDE4D2 structure with inhibitor NPD-417
Resolution2.31 Å
Binding residue
(original residue number in PDB)		M273 I336 M337 F340 M357 Q369 F372
Binding residue
(residue number reindexed from 1)		M186 I249 M250 F253 M270 Q282 F285
Annotation score1
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:6ibf, PDBe:6ibf, PDBj:6ibf
PDBsum6ibf
PubMed
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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