Structure of PDB 8vsg Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: A1AD0
• InChI: InChI=1S/C25H33N3O4/c1-24(2)18-13-28(23(32)25(9-10-25)16-6-4-3-5-7-16)20(19(18)24)22(31)27-17(14-29)12-15-8-11-26-21(15)30/h3-7,15,17-20,29H,8-14H2,1-2H3,(H,26,30)(H,27,31)/t15-,17-,18-,19-,20-/m0/s1
• InChIKey: BJOCSYXAWSVVOR-JBDAPHQKSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1(C2C1C(N(C2)C(=O)C3(CC3)c4ccccc4)C(=O)NC(CC5CCNC5=O)CO)C
  ACDLabs 12.01: CC1(C)C2C(C(=O)NC(CC3CCNC3=O)CO)N(CC21)C(=O)C1(CC1)c1ccccc1
  CACTVS 3.385: CC1(C)[C@H]2CN([C@@H]([C@@H]12)C(=O)N[C@H](CO)C[C@@H]3CCNC3=O)C(=O)C4(CC4)c5ccccc5
  OpenEye OEToolkits 2.0.7: CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C3(CC3)c4ccccc4)C(=O)N[C@@H](C[C@@H]5CCNC5=O)CO)C
  CACTVS 3.385: CC1(C)[CH]2CN([CH]([CH]12)C(=O)N[CH](CO)C[CH]3CCNC3=O)C(=O)C4(CC4)c5ccccc5
• Formula: C25 H33 N3 O4
• Name: (1R,2S,5S)-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-(1-phenylcyclopropane-1-carbonyl)-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 8vsg Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vsg Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity.
• Resolution: 2.071 Å
• Binding residue (original residue number in PDB): H41 F140 G143 C145 H163 H164 M165 E166 Q189
• Binding residue (residue number reindexed from 1): H41 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:8vsg, PDBe:8vsg, PDBj:8vsg
• PDBsum: 8vsg
• PubMed: 38518735
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)