Structure of PDB 5s1a Chain A Binding Site BS01

Receptor Information

>5s1a Chain A (length=165) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WPS
• InChI: InChI=1S/C5H6N4/c1-3-4(2-6)5(7)9-8-3/h1H3,(H3,7,8,9)
• InChIKey: CRRHJAMDQMQGKG-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Cc1n[nH]c(N)c1C#N
  OpenEye OEToolkits 2.0.7: Cc1c(c([nH]n1)N)C#N
  ACDLabs 12.01: n1nc(c(C#N)c1N)C
• Formula: C5 H6 N4
• Name: 5-amino-3-methyl-1H-pyrazole-4-carbonitrile
• ZINC: ZINC000004353708
• PDB chain: 5s1a Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s1a Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.079 Å
• Binding residue (original residue number in PDB): D22 I23 V49 F156
• Binding residue (residue number reindexed from 1): D18 I19 V45 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:5s1a, PDBe:5s1a, PDBj:5s1a
• PDBsum: 5s1a
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)