Structure of PDB 8ifr Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: P0O
• InChI: InChI=1S/C29H47N5O5/c1-16(35)10-11-18(14-17-12-13-30-23(17)36)31-24(37)21-20-19(29(20,8)9)15-34(21)25(38)22(27(2,3)4)32-26(39)33-28(5,6)7/h10-11,17-22H,12-15H2,1-9H3,(H,30,36)(H,31,37)(H2,32,33,39)/b11-10+/t17-,18+,19-,20-,21-,22+/m0/s1
• InChIKey: BKLMFWOPPAUWNX-NWKMKTNDSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(=O)C=CC(CC1CCNC1=O)NC(=O)C2C3C(C3(C)C)CN2C(=O)C(C(C)(C)C)NC(=O)NC(C)(C)C
  CACTVS 3.385: CC(=O)\C=C\[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@@H]2[C@@H]3[C@H](CN2C(=O)[C@@H](NC(=O)NC(C)(C)C)C(C)(C)C)C3(C)C
  OpenEye OEToolkits 2.0.7: CC(=O)C=C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)NC(C)(C)C
  CACTVS 3.385: CC(=O)C=C[CH](C[CH]1CCNC1=O)NC(=O)[CH]2[CH]3[CH](CN2C(=O)[CH](NC(=O)NC(C)(C)C)C(C)(C)C)C3(C)C
• Formula: C29 H47 N5 O5
• Name: (1R,2S,5S)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-N-[(2S)-5-oxidanylidene-1-[(3S)-2-oxidanylidenepyrrolidin-3-yl]hex-3-en-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 8ifr Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ifr Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19
• Resolution: 1.66 Å
• Binding residue (original residue number in PDB): F140 N142 G143 C145 H163 H164 M165 E166 Q189 T190 Q192
• Binding residue (residue number reindexed from 1): F140 N142 G143 C145 H163 H164 M165 E166 Q189 T190 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:8ifr, PDBe:8ifr, PDBj:8ifr
• PDBsum: 8ifr
• PubMed: 37833261
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)