Structure of PDB 8igx Chain A Binding Site BS01

Receptor Information

>8igx Chain A (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: PQL
• InChI: InChI=1S/C22H30F3N5O4S2/c1-20(2,3)15(29-19(34)22(23,24)25)18(33)30-11-21(35-6-7-36-21)9-14(30)17(32)28-13(10-26)8-12-4-5-27-16(12)31/h12-15H,4-9,11H2,1-3H3,(H,27,31)(H,28,32)(H,29,34)/t12-,13-,14-,15+/m0/s1
• InChIKey: LQBRGTAIBBFUJJ-ZQDZILKHSA-N
• SMILES:
  CACTVS 3.385: CC(C)(C)[CH](NC(=O)C(F)(F)F)C(=O)N1CC2(C[CH]1C(=O)N[CH](C[CH]3CCNC3=O)C#N)SCCS2
  CACTVS 3.385: CC(C)(C)[C@H](NC(=O)C(F)(F)F)C(=O)N1CC2(C[C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)SCCS2
  OpenEye OEToolkits 2.0.7: CC(C)(C)C(C(=O)N1CC2(CC1C(=O)NC(CC3CCNC3=O)C#N)SCCS2)NC(=O)C(F)(F)F
  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)C(F)(F)F
• Formula: C22 H30 F3 N5 O4 S2
• Name: (8~{S})-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-7-[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide
• PDB chain: 8igx Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8igx Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): H41 M49 F140 N142 C145 H163 H164 M165 E166 D187 R188 Q189 Q192
• Binding residue (residue number reindexed from 1): H41 M49 F140 N142 C145 H163 H164 M165 E166 D187 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:8igx, PDBe:8igx, PDBj:8igx
• PDBsum: 8igx
• PubMed: 37833261
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)