Structure of PDB 5rvk Chain A Binding Site BS01

Receptor Information

>5rvk Chain A (length=168) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFLE

Ligand information

• Ligand ID: 2AK
• InChI: InChI=1S/C9H6BrNO2/c1-4-2-5-7(6(10)3-4)11-9(13)8(5)12/h2-3H,1H3,(H,11,12,13)
• InChIKey: NPDJRIGMWAQKTQ-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: Brc1cc(cc2c1NC(=O)C2=O)C
  CACTVS 3.370: Cc1cc(Br)c2NC(=O)C(=O)c2c1
  OpenEye OEToolkits 1.7.6: Cc1cc2c(c(c1)Br)NC(=O)C2=O
• Formula: C9 H6 Br N O2
• Name: 7-bromo-5-methyl-1H-indole-2,3-dione
• ChEMBL: CHEMBL3128208
• ZINC: ZINC000002977810
• PDB chain: 5rvk Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rvk Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.46 Å
• Binding residue (original residue number in PDB): V165 S166 L169
• Binding residue (residue number reindexed from 1): V163 S164 L167
• 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.-

External links

• PDB: RCSB:5rvk, PDBe:5rvk, PDBj:5rvk
• PDBsum: 5rvk
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)