Structure of PDB 7ysx Chain B Binding Site BS02

Receptor Information
>7ysx Chain B (length=316) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKI
PVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALVFTDLE
ILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFK
LLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVET
KKVTLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQG
DRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQD
ILDTLEDNREWYQSTI
Ligand information
Ligand IDJU3
InChIInChI=1S/C20H18O6/c1-10(2)3-4-13-15(22)6-5-12(19(13)24)14-9-26-17-8-11(21)7-16(23)18(17)20(14)25/h3,5-9,21-24H,4H2,1-2H3
InChIKeyKCUZCRLRQVRBBV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(=CCc1c(ccc(c1O)C2=COc3cc(cc(c3C2=O)O)O)O)C
CACTVS 3.385CC(C)=CCc1c(O)ccc(c1O)C2=COc3cc(O)cc(O)c3C2=O
FormulaC20 H18 O6
Name3-[3-(3-methylbut-2-enyl)-2,4-bis(oxidanyl)phenyl]-5,7-bis(oxidanyl)chromen-4-one;
Licoisoflavone A
ChEMBLCHEMBL4061300
DrugBank
ZINCZINC000005158963
PDB chain7ysx Chain B 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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PDB7ysx Bioactive compounds from Huashi Baidu decoction possess both antiviral and anti-inflammatory effects against COVID-19.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		M273 Y329 W332 T333 I336 Q369 F372 I376
Binding residue
(residue number reindexed from 1)		M184 Y235 W238 T239 I242 Q275 F278 I282
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:7ysx, PDBe:7ysx, PDBj:7ysx
PDBsum7ysx
PubMed37094153
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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