Structure of PDB 7grg Chain A Binding Site BS01

Receptor Information

>7grg Chain A (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: Y2C
• InChI: InChI=1S/C5H4Cl2N2/c6-3-1-9-2-4(7)5(3)8/h1-2H,(H2,8,9)
• InChIKey: ISIQAMHROGZHOV-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1c(c(c(cn1)Cl)N)Cl
  ACDLabs 12.01: Clc1cncc(Cl)c1N
  CACTVS 3.385: Nc1c(Cl)cncc1Cl
• Formula: C5 H4 Cl2 N2
• Name: 3,5-dichloropyridin-4-amine
• PDB chain: 7grg Chain A Residue 1501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7grg Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
• Resolution: 1.54 Å
• Binding residue (original residue number in PDB): F140 L141 N142 S144 C145 H163 E166
• Binding residue (residue number reindexed from 1): F140 L141 N142 S144 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:7grg, PDBe:7grg, PDBj:7grg
• PDBsum: 7grg
• PubMed: 38289714
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)