Structure of PDB 5sp0 Chain A Binding Site BS01

Receptor Information

>5sp0 Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WY7
• InChI: InChI=1S/C13H10N6O2/c14-12-11-13(16-6-15-11)19(7-17-12)5-8-4-10(21-18-8)9-2-1-3-20-9/h1-4,6-7H,5,14H2
• InChIKey: VMYKOOSLEPKKOO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1cc(oc1)c2cc(no2)Cn3cnc(c-4ncnc34)N
  CACTVS 3.385: Nc1ncn(Cc2cc(on2)c3occc3)c4ncnc14
  ACDLabs 12.01: c4(CN2C=NC(=C1N=CN=C12)N)cc(c3ccco3)on4
• Formula: C13 H10 N6 O2
• Name: 3-{[5-(furan-2-yl)-1,2-oxazol-3-yl]methyl}-3H-purin-6-amine
• PDB chain: 5sp0 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5sp0 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 F156
• Binding residue (residue number reindexed from 1): I21 V47 G128 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:5sp0, PDBe:5sp0, PDBj:5sp0
• PDBsum: 5sp0
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)