Structure of PDB 5rst Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: 5HN
• InChI: InChI=1S/C6H5NO3/c8-5-1-4(6(9)10)2-7-3-5/h1-3,8H,(H,9,10)
• InChIKey: ATTDCVLRGFEHEO-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.370: Oc1cncc(c1)C(O)=O
  ACDLabs 12.01: O=C(O)c1cncc(O)c1
  OpenEye OEToolkits 1.7.6: c1c(cncc1O)C(=O)O
• Formula: C6 H5 N O3
• Name: 5-hydroxypyridine-3-carboxylic acid;
  5-Hydroxynicotinic Acid
• ChEMBL: CHEMBL2146902
• ZINC: ZINC000000332673
• PDB chain: 5rst Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rst 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): G130 F156
• Binding residue (residue number reindexed from 1): G128 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:5rst, PDBe:5rst, PDBj:5rst
• PDBsum: 5rst
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)