Structure of PDB 8ifs Chain B Binding Site BS01

Receptor Information

>8ifs Chain B (length=300) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: OZL
• InChI: InChI=1S/C25H40N6O4S2/c1-23(2,3)18(29-22(35)30-24(4,5)6)21(34)31-14-25(36-9-10-37-25)12-17(31)20(33)28-16(13-26)11-15-7-8-27-19(15)32/h15-18H,7-12,14H2,1-6H3,(H,27,32)(H,28,33)(H2,29,30,35)/t15-,16-,17-,18+/m0/s1
• InChIKey: BLRKRWSWARPDLL-XLAORIBOSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)(C)C(C(=O)N1CC2(CC1C(=O)NC(CC3CCNC3=O)C#N)SCCS2)NC(=O)NC(C)(C)C
  OpenEye OEToolkits 2.0.7: CC(C)(C)[C@@H](C(=O)N1CC2(C[C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)SCCS2)NC(=O)NC(C)(C)C
  CACTVS 3.385: CC(C)(C)NC(=O)N[C@H](C(=O)N1CC2(C[C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)SCCS2)C(C)(C)C
  CACTVS 3.385: CC(C)(C)NC(=O)N[CH](C(=O)N1CC2(C[CH]1C(=O)N[CH](C[CH]3CCNC3=O)C#N)SCCS2)C(C)(C)C
• Formula: C25 H40 N6 O4 S2
• Name: (8~{S})-7-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide
• PDB chain: 8ifs Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ifs Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19
• Resolution: 2.46 Å
• Binding residue (original residue number in PDB): H41 F140 C145 H163 H164 M165 E166 H172 R188 Q189 Q192
• Binding residue (residue number reindexed from 1): H41 F140 C145 H163 H164 M165 E166 H172 R188 Q189 Q192
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:8ifs, PDBe:8ifs, PDBj:8ifs
• PDBsum: 8ifs
• PubMed: 37833261
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)