Structure of PDB 5rt2 Chain A Binding Site BS01

Receptor Information

>5rt2 Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: 5OF
• InChI: InChI=1S/C10H8N2O3/c13-9(14)5-8-6-3-1-2-4-7(6)10(15)12-11-8/h1-4H,5H2,(H,12,15)(H,13,14)
• InChIKey: ZEDQLIHBPGNGEC-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: OC(=O)CC1=NNC(=O)c2ccccc12
  OpenEye OEToolkits 2.0.4: c1ccc2c(c1)C(=NNC2=O)CC(=O)O
• Formula: C10 H8 N2 O3
• Name: 2-(4-oxidanylidene-3~{H}-phthalazin-1-yl)ethanoic acid
• ChEMBL: CHEMBL1411440
• ZINC: ZINC000008652361
• PDB chain: 5rt2 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rt2 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 L160
• Binding residue (residue number reindexed from 1): L124 A127 G128 V153 F154 D155 L158
• 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:5rt2, PDBe:5rt2, PDBj:5rt2
• PDBsum: 5rt2
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)