Structure of PDB 5ss8 Chain A Binding Site BS01

Receptor Information

>5ss8 Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: RLN
• InChI: InChI=1S/C17H14N2O3S/c20-15(21)9-11-1-3-12(4-2-11)10-19-17(22)13-5-7-18-14-6-8-23-16(13)14/h1-8H,9-10H2,(H,19,22)(H,20,21)
• InChIKey: CLXWTDODTCGGCR-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: O=C(O)Cc1ccc(cc1)CNC(=O)c1ccnc2ccsc12
  OpenEye OEToolkits 2.0.7: c1cc(ccc1CC(=O)O)CNC(=O)c2ccnc3c2scc3
  CACTVS 3.385: OC(=O)Cc1ccc(CNC(=O)c2ccnc3ccsc23)cc1
• Formula: C17 H14 N2 O3 S
• Name: (4-{[(thieno[3,2-b]pyridine-7-carbonyl)amino]methyl}phenyl)acetic acid
• PDB chain: 5ss8 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ss8 Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
• Resolution: 1.15 Å
• Binding residue (original residue number in PDB): G130 D157 L160 K163
• Binding residue (residue number reindexed from 1): G128 D155 L158 K161
• 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:5ss8, PDBe:5ss8, PDBj:5ss8
• PDBsum: 5ss8
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)