Structure of PDB 5rv0 Chain A Binding Site BS01

Receptor Information

>5rv0 Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: W6V
• InChI: InChI=1S/C10H8N2OS/c13-9(8-4-2-1-3-5-8)12-10-11-6-7-14-10/h1-7H,(H,11,12,13)
• InChIKey: SCQBDADQAVXTMZ-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)C(=O)Nc2nccs2
  CACTVS 3.385: O=C(Nc1sccn1)c2ccccc2
  ACDLabs 12.01: c2c(C(=O)Nc1nccs1)cccc2
• Formula: C10 H8 N2 O S
• Name: N-(1,3-thiazol-2-yl)benzamide
• ChEMBL: CHEMBL90846
• ZINC: ZINC000000039994
• PDB chain: 5rv0 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rv0 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): A134 D135 P136 L160
• Binding residue (residue number reindexed from 1): A132 D133 P134 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:5rv0, PDBe:5rv0, PDBj:5rv0
• PDBsum: 5rv0
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)