Structure of PDB 7rfr Chain B Binding Site BS01

Receptor Information

>7rfr Chain B (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: 4W8
• InChI: InChI=1S/C32H35N5O5S/c1-32(2)18-15-37(31(41)22-14-17-19(34-22)8-6-9-23(17)42-3)26(25(18)32)29(40)35-21(13-16-11-12-33-28(16)39)27(38)30-36-20-7-4-5-10-24(20)43-30/h4-10,14,16,18,21,25-27,34,38H,11-13,15H2,1-3H3,(H,33,39)(H,35,40)/t16-,18-,21-,25-,26-,27-/m0/s1
• InChIKey: CVWZBMVWUPHSSU-AJEOIHGXSA-N
• SMILES:
  ACDLabs 12.01: COc1cccc2[NH]c(cc12)C(=O)N1CC2C(C1C(=O)NC(CC1CCNC1=O)C(O)c1nc3ccccc3s1)C2(C)C
  OpenEye OEToolkits 2.0.7: CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)c3cc4c([nH]3)cccc4OC)C(=O)N[C@@H](C[C@@H]5CCNC5=O)[C@@H](c6nc7ccccc7s6)O)C
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N3C[CH]4[CH]([CH]3C(=O)N[CH](C[CH]5CCNC5=O)[CH](O)c6sc7ccccc7n6)C4(C)C
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N3C[C@H]4[C@@H]([C@H]3C(=O)N[C@@H](C[C@@H]5CCNC5=O)[C@H](O)c6sc7ccccc7n6)C4(C)C
  OpenEye OEToolkits 2.0.7: CC1(C2C1C(N(C2)C(=O)c3cc4c([nH]3)cccc4OC)C(=O)NC(CC5CCNC5=O)C(c6nc7ccccc7s6)O)C
• Formula: C32 H35 N5 O5 S
• 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-(4-methoxy-1H-indole-2-carbonyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 7rfr Chain B Residue 9001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7rfr An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19.
• Resolution: 1.626 Å
• Binding residue (original residue number in PDB): T25 H41 M49 F140 G143 C145 H163 H164 M165 E166 Q189
• Binding residue (residue number reindexed from 1): T25 H41 M49 F140 G143 C145 H163 H164 M165 E166 Q189
• 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:7rfr, PDBe:7rfr, PDBj:7rfr
• PDBsum: 7rfr
• PubMed: 34726479
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)