Structure of PDB 8dgb Chain B Binding Site BS01

Receptor Information

>8dgb Chain B (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTATAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: B1S
• InChI: InChI=1S/C21H31N3O8S/c1-13(2)10-16(24-21(28)32-12-14-6-4-3-5-7-14)19(26)23-17(20(27)33(29,30)31)11-15-8-9-22-18(15)25/h3-7,13,15-17,20,27H,8-12H2,1-2H3,(H,22,25)(H,23,26)(H,24,28)(H,29,30,31)/t15-,16-,17-,20+/m0/s1
• InChIKey: BSPZFJDYQHDZNR-OGNFBWPZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2ccccc2
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
  ACDLabs 12.01: C(c1ccccc1)OC(=O)NC(C(=O)NC(C(S(=O)(=O)O)O)CC2CCNC2=O)CC(C)C
  OpenEye OEToolkits 2.0.6: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2ccccc2
• Formula: C21 H31 N3 O8 S
• Name: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• ZINC: ZINC000095595103
• PDB chain: 8dgb Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dgb Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.
• Resolution: 2.87 Å
• Binding residue (original residue number in PDB): N142 C145 H163 H164 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): N142 C145 H163 H164 M165 E166 D187 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:8dgb, PDBe:8dgb, PDBj:8dgb
• PDBsum: 8dgb
• PubMed: 37637734
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)