Structure of PDB 5ruy Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: XAN
• InChI: InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)
• InChIKey: LRFVTYWOQMYALW-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: O=C1NC(=O)c2nc[nH]c2N1
  OpenEye OEToolkits 1.5.0: c1[nH]c2c(n1)C(=O)NC(=O)N2
  ACDLabs 10.04: O=C2c1ncnc1NC(=O)N2
• Formula: C5 H4 N4 O2
• Name: XANTHINE
• ChEMBL: CHEMBL1424
• DrugBank: DB02134
• ZINC: ZINC000013517187
• PDB chain: 5ruy Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ruy 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): D22 I23 V49 A52 F156
• Binding residue (residue number reindexed from 1): D20 I21 V47 A50 F154
• 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:5ruy, PDBe:5ruy, PDBj:5ruy
• PDBsum: 5ruy
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)