Structure of PDB 5s1w Chain A Binding Site BS01

Receptor Information

>5s1w Chain A (length=165) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WQV
• InChI: InChI=1S/C7H7BrN2O2/c1-4(11)10-6-2-5(8)3-9-7(6)12/h2-3H,1H3,(H,9,12)(H,10,11)
• InChIKey: DZPXAAPHBCJNCQ-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: N1C(=O)C(NC(=O)C)=CC(=C1)Br
  CACTVS 3.385
  OpenEye OEToolkits 2.0.7: CC(=O)NC1=CC(=CNC1=O)Br
• Formula: C7 H7 Br N2 O2
• Name: N-(5-bromo-2-oxo-1,2-dihydropyridin-3-yl)acetamide
• ZINC: ZINC000067936997
• PDB chain: 5s1w Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s1w Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.135 Å
• Binding residue (original residue number in PDB): D22 V49 A52 F156
• Binding residue (residue number reindexed from 1): D18 V45 A48 F152
• 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:5s1w, PDBe:5s1w, PDBj:5s1w
• PDBsum: 5s1w
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)