Structure of PDB 5s3j Chain A Binding Site BS01

Receptor Information

>5s3j Chain A (length=164) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSF

Ligand information

• Ligand ID: W1S
• InChI: InChI=1S/C8H11N3O/c9-7(12)6-2-1-4-11-5-3-10-8(6)11/h3,5-6H,1-2,4H2,(H2,9,12)/t6-/m1/s1
• InChIKey: VSXNZKCCQSDVAD-ZCFIWIBFSA-N
• SMILES:
  CACTVS 3.385: NC(=O)[CH]1CCCn2ccnc12
  CACTVS 3.385: NC(=O)[C@H]1CCCn2ccnc12
  ACDLabs 12.01: n21CCCC(c1ncc2)C(=O)N
  OpenEye OEToolkits 2.0.7: c1cn2c(n1)C(CCC2)C(=O)N
  OpenEye OEToolkits 2.0.7: c1cn2c(n1)[C@H](CCC2)C(=O)N
• Formula: C8 H11 N3 O
• Name: (8S)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-8-carboxamide
• ZINC: ZINC000075772338
• PDB chain: 5s3j Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s3j Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.087 Å
• Binding residue (original residue number in PDB): D22 G48 V49 F156
• Binding residue (residue number reindexed from 1): D18 G44 V45 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:5s3j, PDBe:5s3j, PDBj:5s3j
• PDBsum: 5s3j
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)