Structure of PDB 6kjz Chain A Binding Site BS02

Receptor Information
>6kjz Chain A (length=327) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKT
FKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAV
FTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHL
AVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLK
TMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTD
RIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETW
ADLVHPDAQDILDTLEDNREWYQSTIP
Ligand information
Ligand IDMKU
InChIInChI=1S/C24H26O6/c1-12(2)6-7-14-19-17(10-15(25)23(14)28-5)29-18-11-16-13(8-9-24(3,4)30-16)21(26)20(18)22(19)27/h6,10-11,25-26H,7-9H2,1-5H3
InChIKeyKJCDBAVVDILRMP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC(=CCc1c2c(cc(c1OC)O)Oc3cc4c(c(c3C2=O)O)CCC(O4)(C)C)C
CACTVS 3.385COc1c(O)cc2Oc3cc4OC(C)(C)CCc4c(O)c3C(=O)c2c1CC=C(C)C
ACDLabs 12.01C\C(=C/Cc4c3C(c2c(c1CCC(C)(C)Oc1cc2Oc3cc(O)c4OC)O)=O)C
FormulaC24 H26 O6
Name5,9-dihydroxy-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H,6H-pyrano[3,2-b]xanthen-6-one;
3-isomangostin
ChEMBLCHEMBL464119
DrugBank
ZINCZINC000013382496
PDB chain6kjz Chain A Residue 503 [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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PDB6kjz Discovery and Optimization of alpha-Mangostin Derivatives as Novel PDE4 Inhibitors for the Treatment of Vascular Dementia.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		P322 W332 I336 M357 Q369 F372
Binding residue
(residue number reindexed from 1)		P238 W248 I252 M273 Q285 F288
Annotation score1
Binding affinityMOAD: ic50=420nM
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:6kjz, PDBe:6kjz, PDBj:6kjz
PDBsum6kjz
PubMed32115956
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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