Structure of PDB 5rth Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: 3BZ
• InChI: InChI=1S/C7H5ClO2/c8-6-3-1-2-5(4-6)7(9)10/h1-4H,(H,9,10)
• InChIKey: LULAYUGMBFYYEX-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)c1cc(Cl)ccc1
  CACTVS 3.341: OC(=O)c1cccc(Cl)c1
  OpenEye OEToolkits 1.5.0: c1cc(cc(c1)Cl)C(=O)O
• Formula: C7 H5 Cl O2
• Name: 3-chlorobenzoate
• ChEMBL: CHEMBL20563
• ZINC: ZINC000000156863
• PDB chain: 5rth Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rth 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): D22 G48 V49 F156
• Binding residue (residue number reindexed from 1): D20 G46 V47 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:5rth, PDBe:5rth, PDBj:5rth
• PDBsum: 5rth
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)