Structure of PDB 5s4i Chain A Binding Site BS01

Receptor Information

>5s4i Chain A (length=165) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSFL

Ligand information

• Ligand ID: W3Y
• InChI: InChI=1S/C10H9ClN2O2/c1-6-9(14)12-10(15)13(6)8-4-2-7(11)3-5-8/h2-6H,1H3,(H,12,14,15)/t6-/m0/s1
• InChIKey: YRTFBBSKIRZNAW-LURJTMIESA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C[C@H]1C(=O)NC(=O)N1c2ccc(cc2)Cl
  ACDLabs 12.01: N2C(N(c1ccc(cc1)Cl)C(C2=O)C)=O
  OpenEye OEToolkits 2.0.7: CC1C(=O)NC(=O)N1c2ccc(cc2)Cl
  CACTVS 3.385: C[CH]1N(C(=O)NC1=O)c2ccc(Cl)cc2
  CACTVS 3.385: C[C@@H]1N(C(=O)NC1=O)c2ccc(Cl)cc2
• Formula: C10 H9 Cl N2 O2
• Name: (5S)-1-(4-chlorophenyl)-5-methylimidazolidine-2,4-dione
• ZINC: ZINC000004219004
• PDB chain: 5s4i Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s4i Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.131 Å
• Binding residue (original residue number in PDB): G130 F156 D157
• Binding residue (residue number reindexed from 1): G126 F152 D153
• 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:5s4i, PDBe:5s4i, PDBj:5s4i
• PDBsum: 5s4i
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)