Structure of PDB 7grj Chain A Binding Site BS01

Receptor Information

>7grj Chain A (length=302) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG

Ligand information

• Ligand ID: Y1L
• InChI: InChI=1S/C9H7ClOS/c10-7-1-2-9-8(3-7)6(4-11)5-12-9/h1-3,5,11H,4H2
• InChIKey: PUSCUZZEDIEHOQ-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1cc2c(cc1Cl)c(cs2)CO
  CACTVS 3.385: OCc1csc2ccc(Cl)cc12
  ACDLabs 12.01: Clc1cc2c(cc1)scc2CO
• Formula: C9 H7 Cl O S
• Name: (5-chloro-1-benzothiophen-3-yl)methanol
• PDB chain: 7grj Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7grj Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
• Resolution: 1.74 Å
• Binding residue (original residue number in PDB): H41 M49 H164 M165 D187 R188 Q189
• Binding residue (residue number reindexed from 1): H41 M49 H164 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:7grj, PDBe:7grj, PDBj:7grj
• PDBsum: 7grj
• PubMed: 38289714
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)