Structure of PDB 7gs2 Chain A Binding Site BS01

Receptor Information

>7gs2 Chain A (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: 5F8
• InChI: InChI=1S/C12H9NO2/c14-12(15)10-4-1-3-9(7-10)11-5-2-6-13-8-11/h1-8H,(H,14,15)
• InChIKey: PXASTGBSGPFLFJ-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1cc(cc(c1)C(=O)O)c2cccnc2
  ACDLabs 12.01
  CACTVS 3.385: OC(=O)c1cccc(c1)c2cccnc2
• Formula: C12 H9 N O2
• Name: 3-(pyridin-3-yl)benzoic acid
• ChEMBL: CHEMBL3896367
• ZINC: ZINC000002581037
• PDB chain: 7gs2 Chain A Residue 1501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7gs2 Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
• Resolution: 1.77 Å
• Binding residue (original residue number in PDB): P184 R188 Q192
• Binding residue (residue number reindexed from 1): P184 R188 Q192
• 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:7gs2, PDBe:7gs2, PDBj:7gs2
• PDBsum: 7gs2
• PubMed: 38289714
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)