Structure of PDB 5s2i Chain B Binding Site BS01

Receptor Information

>5s2i Chain B (length=169) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVA
GALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNV
NKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTN
VYLAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: LUY
• InChI: InChI=1S/C15H15N3/c1-2-6-12(7-3-1)10-11-16-15-17-13-8-4-5-9-14(13)18-15/h1-9H,10-11H2,(H2,16,17,18)
• InChIKey: OWETVOGOOABRTJ-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)CCNc2[nH]c3ccccc3n2
  CACTVS 3.385: C(Cc1ccccc1)Nc2[nH]c3ccccc3n2
• Formula: C15 H15 N3
• Name: ~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine
• ZINC: ZINC000000513006
• PDB chain: 5s2i Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s2i Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.085 Å
• Binding residue (original residue number in PDB): A134 D135 P136 D157 N159 L160
• Binding residue (residue number reindexed from 1): A134 D135 P136 D157 N159 L160
• 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:5s2i, PDBe:5s2i, PDBj:5s2i
• PDBsum: 5s2i
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)