Structure of PDB 5s1k Chain A Binding Site BS01

Receptor Information

>5s1k Chain A (length=165) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WQ7
• InChI: InChI=1S/C7H10N2O/c8-4-6-9-5-2-1-3-7(9)10/h1-3,5H,4,6,8H2
• InChIKey: IZSOENLZRWXCER-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: NCCN1C(C=CC=C1)=O
  OpenEye OEToolkits 2.0.7: C1=CC(=O)N(C=C1)CCN
  CACTVS 3.385: NCCN1C=CC=CC1=O
• Formula: C7 H10 N2 O
• Name: 1-(2-aminoethyl)pyridin-2(1H)-one
• ChEMBL: CHEMBL4578665
• ZINC: ZINC000022220049
• PDB chain: 5s1k Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s1k Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.076 Å
• Binding residue (original residue number in PDB): D22 G48 V49 A52 F156
• Binding residue (residue number reindexed from 1): D18 G44 V45 A48 F152
• 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:5s1k, PDBe:5s1k, PDBj:5s1k
• PDBsum: 5s1k
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)