Structure of PDB 7grq Chain A Binding Site BS01

Receptor Information

>7grq Chain A (length=300) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: Y0S
• InChI: InChI=1S/C13H13NOS/c1-10-7-8-16-12(10)9-14-13(15)11-5-3-2-4-6-11/h2-8H,9H2,1H3,(H,14,15)
• InChIKey: WNIZEKJOPGQRGN-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385
  OpenEye OEToolkits 2.0.7: Cc1ccsc1CNC(=O)c2ccccc2
  ACDLabs 12.01: Cc1ccsc1CNC(=O)c1ccccc1
• Formula: C13 H13 N O S
• Name: N-[(3-methylthiophen-2-yl)methyl]benzamide
• PDB chain: 7grq Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7grq Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): H41 C44 S46 M49 M165 D187 R188 Q189
• Binding residue (residue number reindexed from 1): H41 C44 S46 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:7grq, PDBe:7grq, PDBj:7grq
• PDBsum: 7grq
• PubMed: 38289714
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)