Structure of PDB 7gro Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: Y3N
• InChI: InChI=1S/C10H7F3N2O/c1-6(16)15-9-3-2-7(5-14)4-8(9)10(11,12)13/h2-4H,1H3,(H,15,16)
• InChIKey: OBFBGHKUUCGSPC-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385
  OpenEye OEToolkits 2.0.7: CC(=O)Nc1ccc(cc1C(F)(F)F)C#N
  ACDLabs 12.01: O=C(C)Nc1ccc(cc1C(F)(F)F)C#N
• Formula: C10 H7 F3 N2 O
• Name: N-[4-cyano-2-(trifluoromethyl)phenyl]acetamide
• PDB chain: 7gro Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7gro Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): H41 M49 M165 D187 R188 Q189
• Binding residue (residue number reindexed from 1): H41 M49 M165 D187 R188 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:7gro, PDBe:7gro, PDBj:7gro
• PDBsum: 7gro
• PubMed: 38289714
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)