Structure of PDB 5spx Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: QIW
• InChI: InChI=1S/C15H16N4O2/c1-4-9-6-16-14-11(9)5-10(7-17-14)13-12(15(20)21)8(2)18-19(13)3/h5-7H,4H2,1-3H3,(H,16,17)(H,20,21)
• InChIKey: CJCWGFRSMPSRDX-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CCc1c[nH]c2ncc(cc12)c3n(C)nc(C)c3C(O)=O
  OpenEye OEToolkits 2.0.7: CCc1c[nH]c2c1cc(cn2)c3c(c(nn3C)C)C(=O)O
  ACDLabs 12.01: OC(=O)c1c(c2cc3c(CC)c[NH]c3nc2)n(C)nc1C
• Formula: C15 H16 N4 O2
• Name: (5M)-5-(3-ethyl-1H-pyrrolo[2,3-b]pyridin-5-yl)-1,3-dimethyl-1H-pyrazole-4-carboxylic acid
• PDB chain: 5spx Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5spx Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
• Resolution: 1.05 Å
• Binding residue (original residue number in PDB): A129 G130 V155 F156
• Binding residue (residue number reindexed from 1): A127 G128 V153 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:5spx, PDBe:5spx, PDBj:5spx
• PDBsum: 5spx
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)