Structure of PDB 7gri Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: Y1R
• InChI: InChI=1S/C5H8N2O/c1-4(8)5-2-3-6-7-5/h2-4,8H,1H3,(H,6,7)/t4-/m0/s1
• InChIKey: CABHXTNYNGUYFF-BYPYZUCNSA-N
• SMILES:
  ACDLabs 12.01: CC(O)c1ccn[NH]1
  OpenEye OEToolkits 2.0.7: C[C@@H](c1ccn[nH]1)O
  CACTVS 3.385: C[C@H](O)c1[nH]ncc1
  OpenEye OEToolkits 2.0.7: CC(c1ccn[nH]1)O
  CACTVS 3.385: C[CH](O)c1[nH]ncc1
• Formula: C5 H8 N2 O
• Name: (1S)-1-(1H-pyrazol-5-yl)ethan-1-ol
• PDB chain: 7gri Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7gri Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
• Resolution: 1.79 Å
• Binding residue (original residue number in PDB): F140 L141 N142 H163 E166
• Binding residue (residue number reindexed from 1): F140 L141 N142 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:7gri, PDBe:7gri, PDBj:7gri
• PDBsum: 7gri
• PubMed: 38289714
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)