Structure of PDB 7xaa Chain A Binding Site BS02

Receptor Information
>7xaa Chain A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTF
KIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVF
TDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLA
VGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKT
MVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDR
IMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWA
DLVHPDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDAQL
InChIInChI=1S/C30H29NO6/c1-17(2)6-7-20-25-23(14-21(32)28(20)34-5)36-24-15-22-19(8-11-30(3,4)37-22)29(26(24)27(25)33)35-16-18-9-12-31-13-10-18/h6,8-15,32H,7,16H2,1-5H3
InChIKeyREKLCXXJHWMMFP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1c(O)cc2Oc3cc4OC(C)(C)C=Cc4c(OCc5ccncc5)c3C(=O)c2c1CC=C(C)C
OpenEye OEToolkits 2.0.7CC(=CCc1c2c(cc(c1OC)O)Oc3cc4c(c(c3C2=O)OCc5ccncc5)C=CC(O4)(C)C)C
FormulaC30 H29 N O6
Name8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-9-oxidanyl-5-(pyridin-4-ylmethoxy)pyrano[3,2-b]xanthen-6-one
ChEMBL
DrugBank
ZINC
PDB chain7xaa Chain A Residue 603 [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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PDB7xaa Discovery of novel PDE4 inhibitors targeting the M-pocket from natural mangostanin with improved safety for the treatment of Inflammatory Bowel Diseases.
Resolution2.10041 Å
Binding residue
(original residue number in PDB)		M273 P322 I336 M357 F372
Binding residue
(residue number reindexed from 1)		M188 P237 I251 M272 F287
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:7xaa, PDBe:7xaa, PDBj:7xaa
PDBsum7xaa
PubMed35985255
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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