Structure of PDB 5s1u Chain A Binding Site BS01

Receptor Information

>5s1u Chain A (length=165) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WQM
• InChI: InChI=1S/C7H8N2O2/c1-8-7(11)5-2-3-6(10)9-4-5/h2-5H,1H3,(H,8,11)/t5-/m0/s1
• InChIKey: VENCKILMSBWPLT-YFKPBYRVSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CNC(=O)C1C=CC(=O)N=C1
  CACTVS 3.385: CNC(=O)[C@H]1C=CC(=O)N=C1
  ACDLabs 12.01: N(C)C(=O)C1C=CC(N=C1)=O
  CACTVS 3.385: CNC(=O)[CH]1C=CC(=O)N=C1
• Formula: C7 H8 N2 O2
• Name: (3S)-N-methyl-6-oxo-3,6-dihydropyridine-3-carboxamide
• PDB chain: 5s1u Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s1u Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.08 Å
• Binding residue (original residue number in PDB): D22 I23 V49 A52 F156
• Binding residue (residue number reindexed from 1): D18 I19 V45 A48 F152
• 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:5s1u, PDBe:5s1u, PDBj:5s1u
• PDBsum: 5s1u
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)