Structure of PDB 5rtp Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: AOT
• InChI: InChI=1S/C8H7NO3/c10-7(8(11)12)9-6-4-2-1-3-5-6/h1-5H,(H,9,10)(H,11,12)
• InChIKey: PQJZHMCWDKOPQG-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)NC(=O)C(=O)O
  CACTVS 3.385: OC(=O)C(=O)Nc1ccccc1
• Formula: C8 H7 N O3
• Name: 2-oxidanylidene-2-phenylazanyl-ethanoic acid
• ChEMBL: CHEMBL3248231
• ZINC: ZINC000001679336
• PDB chain: 5rtp Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rtp 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): V155 F156 L160
• Binding residue (residue number reindexed from 1): V153 F154 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:5rtp, PDBe:5rtp, PDBj:5rtp
• PDBsum: 5rtp
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)