Structure of PDB 7grf Chain B Binding Site BS01

Receptor Information

>7grf Chain B (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: XWZ
• InChI: InChI=1S/C5H5BrN2/c6-4-1-5(7)3-8-2-4/h1-3H,7H2
• InChIKey: MDQXGHBCDCOOSM-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01
  CACTVS 3.385: Nc1cncc(Br)c1
  OpenEye OEToolkits 2.0.7: c1c(cncc1Br)N
• Formula: C5 H5 Br N2
• Name: 5-bromopyridin-3-amine
• PDB chain: 7grf Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7grf Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
• Resolution: 1.84 Å
• Binding residue (original residue number in PDB): F140 L141 N142 C145 H163 E166
• Binding residue (residue number reindexed from 1): F140 L141 N142 C145 H163 E166
• 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:7grf, PDBe:7grf, PDBj:7grf
• PDBsum: 7grf
• PubMed: 38289714
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)