Structure of PDB 5sos Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WWS
• InChI: InChI=1S/C11H9ClN6/c12-7-1-2-8(14-3-7)4-18-6-17-10(13)9-11(18)16-5-15-9/h1-3,5-6H,4,13H2
• InChIKey: RILIKBFMMNNYNO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1cc(ncc1Cl)Cn2cnc(c-3ncnc23)N
  CACTVS 3.385: Nc1ncn(Cc2ccc(Cl)cn2)c3ncnc13
  ACDLabs 12.01: c1(ncc(cc1)Cl)CN3C=NC(=C2N=CN=C23)N
• Formula: C11 H9 Cl N6
• Name: 3-[(5-chloropyridin-2-yl)methyl]-3H-purin-6-amine
• PDB chain: 5sos Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5sos 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 L126 A129 F156
• Binding residue (residue number reindexed from 1): I21 V47 L124 A127 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:5sos, PDBe:5sos, PDBj:5sos
• PDBsum: 5sos
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)