Structure of PDB 6kjz Chain B Binding Site BS02

Receptor Information
>6kjz Chain B (length=328) 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
ADLVHPDAQDILDTLEDNREWYQSTIPQ
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 B 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)		M273 P322 T333 I336 M357 Q369 F372
Binding residue
(residue number reindexed from 1)		M189 P238 T249 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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