Structure of PDB 7rfu Chain A Binding Site BS01

Receptor Information

>7rfu Chain A (length=299) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLN
PNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: 4YG
• InChI: InChI=1S/C28H39N5O6S2/c1-14(2)21(32-41(5,38)39)27(37)33-13-16-20(28(16,3)4)22(33)25(36)30-18(12-15-10-11-29-24(15)35)23(34)26-31-17-8-6-7-9-19(17)40-26/h6-9,14-16,18,20-23,32,34H,10-13H2,1-5H3,(H,29,35)(H,30,36)/t15-,16-,18-,20-,21-,22-,23-/m0/s1
• InChIKey: FSCAOQMZHZLHRY-DECHFVIOSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)[C@@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](c4nc5ccccc5s4)O)C2(C)C)NS(=O)(=O)C
  CACTVS 3.385: CC(C)[C@H](N[S](C)(=O)=O)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)c4sc5ccccc5n4)C2(C)C
  OpenEye OEToolkits 2.0.7: CC(C)C(C(=O)N1CC2C(C1C(=O)NC(CC3CCNC3=O)C(c4nc5ccccc5s4)O)C2(C)C)NS(=O)(=O)C
  ACDLabs 12.01: CC(C)C(NS(C)(=O)=O)C(=O)N1CC2C(C1C(=O)NC(CC1CCNC1=O)C(O)c1nc3ccccc3s1)C2(C)C
  CACTVS 3.385: CC(C)[CH](N[S](C)(=O)=O)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)c4sc5ccccc5n4)C2(C)C
• Formula: C28 H39 N5 O6 S2
• Name: (1R,2S,5S)-N-{(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-3-[N-(methanesulfonyl)-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 7rfu Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7rfu An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19.
• Resolution: 2.498 Å
• Binding residue (original residue number in PDB): H41 M49 F140 N142 G143 S144 C145 H163 H164 M165 E166 Q189 T190
• Binding residue (residue number reindexed from 1): H40 M48 F139 N141 G142 S143 C144 H162 H163 M164 E165 Q188 T189
• 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:7rfu, PDBe:7rfu, PDBj:7rfu
• PDBsum: 7rfu
• PubMed: 34726479
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)