Structure of PDB 5soz Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WXY
• InChI: InChI=1S/C16H20N4O/c21-15(13-12-5-9-17-14(12)19-11-18-13)20-10-4-8-16(20)6-2-1-3-7-16/h5,9,11H,1-4,6-8,10H2,(H,17,18,19)
• InChIKey: VQJWUFYETGKQGL-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: O=C(N1CCCC12CCCCC2)c3ncnc4[nH]ccc34
  OpenEye OEToolkits 2.0.7: c1c[nH]c2c1c(ncn2)C(=O)N3CCCC34CCCCC4
  ACDLabs 12.01: C4CCC3(CCCN3C(c2c1c(ncc1)ncn2)=O)CC4
• Formula: C16 H20 N4 O
• Name: (1-azaspiro[4.5]decan-1-yl)(7H-pyrrolo[2,3-d]pyrimidin-4-yl)methanone
• PDB chain: 5soz Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5soz 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): I23 V49 G130 A154 F156
• Binding residue (residue number reindexed from 1): I21 V47 G128 A152 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:5soz, PDBe:5soz, PDBj:5soz
• PDBsum: 5soz
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)