Structure of PDB 5spn Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: S50
• InChI: InChI=1S/C16H19N5O2S/c1-11-8-15(21(19-11)14-4-2-3-5-14)24(22,23)20-13-9-12-6-7-17-16(12)18-10-13/h6-10,14,20H,2-5H2,1H3,(H,17,18)
• InChIKey: RJFXVLMCNRXHDX-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Cc1cc(n(n1)C2CCCC2)[S](=O)(=O)Nc3cnc4[nH]ccc4c3
  OpenEye OEToolkits 2.0.7: Cc1cc(n(n1)C2CCCC2)S(=O)(=O)Nc3cc4cc[nH]c4nc3
  ACDLabs 12.01: O=S(=O)(Nc1cc2cc[NH]c2nc1)c1cc(C)nn1C1CCCC1
• Formula: C16 H19 N5 O2 S
• Name: 1-cyclopentyl-3-methyl-N-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazole-5-sulfonamide
• PDB chain: 5spn Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5spn 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): D22 G130 F156 D157
• Binding residue (residue number reindexed from 1): D20 G128 F154 D155
• 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:5spn, PDBe:5spn, PDBj:5spn
• PDBsum: 5spn
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)