Structure of PDB 5rve Chain A Binding Site BS01

Receptor Information

>5rve Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: W8A
• InChI: InChI=1S/C8H12N2O4S/c1-5(15-4-6(11)12)7(13)10-3-2-9-8(10)14/h5H,2-4H2,1H3,(H,9,14)(H,11,12)/t5-/m0/s1
• InChIKey: VUVWCZPJVQECKW-YFKPBYRVSA-N
• SMILES:
  CACTVS 3.385: C[C@H](SCC(O)=O)C(=O)N1CCNC1=O
  CACTVS 3.385: C[CH](SCC(O)=O)C(=O)N1CCNC1=O
  OpenEye OEToolkits 2.0.7: CC(C(=O)N1CCNC1=O)SCC(=O)O
  OpenEye OEToolkits 2.0.7: C[C@@H](C(=O)N1CCNC1=O)SCC(=O)O
  ACDLabs 12.01: CC(C(N1CCNC1=O)=O)SCC(=O)O
• Formula: C8 H12 N2 O4 S
• Name: {[(2S)-1-oxo-1-(2-oxoimidazolidin-1-yl)propan-2-yl]sulfanyl}acetic acid
• PDB chain: 5rve Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rve Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.0 Å
• Binding residue (original residue number in PDB): G48 V49 V155 F156 D157 L160
• Binding residue (residue number reindexed from 1): G46 V47 V153 F154 D155 L158
• 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:5rve, PDBe:5rve, PDBj:5rve
• PDBsum: 5rve
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)