Structure of PDB 7lyi Chain A Binding Site BS01

Receptor Information

>7lyi Chain A (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLN
PNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS
GVTF

Ligand information

• Ligand ID: YHI
• InChI: InChI=1S/C23H31N3O5/c1-23(2)17-11-26(22(30)31-13-14-6-4-3-5-7-14)19(18(17)23)21(29)25-16(12-27)10-15-8-9-24-20(15)28/h3-7,15-19,27H,8-13H2,1-2H3,(H,24,28)(H,25,29)/t15-,16-,17-,18-,19-/m0/s1
• InChIKey: KXNVRILCTPCDNL-VMXHOPILSA-N
• SMILES:
  ACDLabs 12.01: O=C1NCCC1CC(CO)NC(=O)C1C2C(CN1C(=O)OCc1ccccc1)C2(C)C
  CACTVS 3.385: CC1(C)[CH]2CN([CH]([CH]12)C(=O)N[CH](CO)C[CH]3CCNC3=O)C(=O)OCc4ccccc4
  OpenEye OEToolkits 2.0.7: CC1(C2C1C(N(C2)C(=O)OCc3ccccc3)C(=O)NC(CC4CCNC4=O)CO)C
  OpenEye OEToolkits 2.0.7: CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)OCc3ccccc3)C(=O)N[C@@H](C[C@@H]4CCNC4=O)CO)C
  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)OCc4ccccc4
• Formula: C23 H31 N3 O5
• Name: benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate
• PDB chain: 7lyi Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lyi Rational Design of Hybrid SARS-CoV-2 Main Protease Inhibitors Guided by the Superimposed Cocrystal Structures with the Peptidomimetic Inhibitors GC-376, Telaprevir, and Boceprevir.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 D187
• Binding residue (residue number reindexed from 1): H40 M48 F139 N141 G142 C144 H162 H163 M164 E165 D186
• 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:7lyi, PDBe:7lyi, PDBj:7lyi
• PDBsum: 7lyi
• PubMed: 34414360
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)