Structure of PDB 5rua Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: 3EU
• InChI: InChI=1S/C8H6Cl2O2/c9-6-1-5(3-8(11)12)2-7(10)4-6/h1-2,4H,3H2,(H,11,12)
• InChIKey: RERINLRFXYGZEE-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: Clc1cc(cc(Cl)c1)CC(=O)O
  OpenEye OEToolkits 1.7.6: c1c(cc(cc1Cl)Cl)CC(=O)O
  CACTVS 3.385: OC(=O)Cc1cc(Cl)cc(Cl)c1
• Formula: C8 H6 Cl2 O2
• Name: (3,5-dichlorophenyl)acetic acid
• ZINC: ZINC000033986325
• PDB chain: 5rua Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rua 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): L126 A129 G130 V155 F156 D157
• Binding residue (residue number reindexed from 1): L124 A127 G128 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:5rua, PDBe:5rua, PDBj:5rua
• PDBsum: 5rua
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)