Structure of PDB 8yrh Chain A Binding Site BS01

Receptor Information

>8yrh Chain A (length=296) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLAGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVR

Ligand information

• Ligand ID: ROA
• InChI: InChI=1S/C18H16O8/c19-12-4-1-10(7-14(12)21)3-6-17(23)26-16(18(24)25)9-11-2-5-13(20)15(22)8-11/h1-8,16,19-22H,9H2,(H,24,25)/b6-3+/t16-/m1/s1
• InChIKey: DOUMFZQKYFQNTF-WUTVXBCWSA-N
• SMILES:
  ACDLabs 12.01: O=C(O)C(OC(=O)\C=C\c1ccc(O)c(O)c1)Cc2cc(O)c(O)cc2
  OpenEye OEToolkits 1.7.6: c1cc(c(cc1C[C@H](C(=O)O)OC(=O)/C=C/c2ccc(c(c2)O)O)O)O
  CACTVS 3.385: OC(=O)[CH](Cc1ccc(O)c(O)c1)OC(=O)C=Cc2ccc(O)c(O)c2
  CACTVS 3.385: OC(=O)[C@@H](Cc1ccc(O)c(O)c1)OC(=O)\C=C\c2ccc(O)c(O)c2
  OpenEye OEToolkits 1.7.6: c1cc(c(cc1CC(C(=O)O)OC(=O)C=Cc2ccc(c(c2)O)O)O)O
• Formula: C18 H16 O8
• Name: (2R)-3-(3,4-dihydroxyphenyl)-2-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}propanoic acid;
  Rosmarinic acid
• ChEMBL: CHEMBL324842
• DrugBank: DB16865
• ZINC: ZINC000000899870
• PDB chain: 8yrh Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8yrh Structural basis of rosmarinic acid inhibitory mechanism on SARS-CoV-2 main protease.
• Resolution: 1.841 Å
• Binding residue (original residue number in PDB): T24 T25 C44 T45 S46 M49 C145 M165 E166 Q189
• Binding residue (residue number reindexed from 1): T22 T23 C42 T43 S44 M47 C143 M163 E164 Q187
• Annotation score: 1

External links

• PDB: RCSB:8yrh, PDBe:8yrh, PDBj:8yrh
• PDBsum: 8yrh
• PubMed: 38865813
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)