Structure of PDB 5s2k Chain B Binding Site BS01

Receptor Information

>5s2k Chain B (length=169) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVA
GALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNV
NKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTN
VYLAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: VZP
• InChI: InChI=1S/C9H18N2O3S/c1-7(2)10-9(12)11(3)8-4-5-15(13,14)6-8/h7-8H,4-6H2,1-3H3,(H,10,12)/t8-/m1/s1
• InChIKey: RMWFRPZNASSVCZ-MRVPVSSYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)NC(=O)N(C)C1CCS(=O)(=O)C1
  CACTVS 3.385: CC(C)NC(=O)N(C)[C@@H]1CC[S](=O)(=O)C1
  ACDLabs 12.01: N(C1CCS(C1)(=O)=O)(C(=O)NC(C)C)C
  CACTVS 3.385: CC(C)NC(=O)N(C)[CH]1CC[S](=O)(=O)C1
  OpenEye OEToolkits 2.0.7: CC(C)NC(=O)N(C)[C@@H]1CCS(=O)(=O)C1
• Formula: C9 H18 N2 O3 S
• Name: N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-methyl-N'-propan-2-ylurea
• ZINC: ZINC000042838879
• PDB chain: 5s2k Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s2k Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.097 Å
• Binding residue (original residue number in PDB): Q107 L108
• Binding residue (residue number reindexed from 1): Q107 L108
• 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:5s2k, PDBe:5s2k, PDBj:5s2k
• PDBsum: 5s2k
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)