Structure of PDB 5rt3 Chain A Binding Site BS01

Receptor Information

>5rt3 Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: 2FX
• InChI: InChI=1S/C10H8O2S/c11-10(12)6-8-5-7-3-1-2-4-9(7)13-8/h1-5H,6H2,(H,11,12)
• InChIKey: SAAWNQLNUJBOLW-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1ccc2c(c1)cc(s2)CC(=O)O
  CACTVS 3.352: OC(=O)Cc1sc2ccccc2c1
  ACDLabs 11.02: O=C(O)Cc2sc1ccccc1c2
• Formula: C10 H8 O2 S
• Name: 1-benzothiophen-2-ylacetic acid
• ZINC: ZINC000039281982
• PDB chain: 5rt3 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rt3 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.05 Å
• Binding residue (original residue number in PDB): A129 G130 F132 V155 F156 D157
• Binding residue (residue number reindexed from 1): A127 G128 F130 V153 F154 D155
• 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:5rt3, PDBe:5rt3, PDBj:5rt3
• PDBsum: 5rt3
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)