Structure of PDB 5rul Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: 5ZE
• InChI: InChI=1S/C6H9N3/c1-4-3-5(2)9-6(7)8-4/h3H,1-2H3,(H2,7,8,9)
• InChIKey: IDQNBVFPZMCDDN-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Cc1cc(C)nc(N)n1
  OpenEye OEToolkits 1.7.6: Cc1cc(nc(n1)N)C
  ACDLabs 12.01: n1c(cc(nc1N)C)C
• Formula: C6 H9 N3
• Name: 4,6-dimethylpyrimidin-2-amine
• ChEMBL: CHEMBL4546836
• ZINC: ZINC000000163774
• PDB chain: 5rul Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rul 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 G48 A52 F156
• Binding residue (residue number reindexed from 1): D20 G46 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:5rul, PDBe:5rul, PDBj:5rul
• PDBsum: 5rul
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)