Structure of PDB 5ssa Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: RM6
• InChI: InChI=1S/C15H16N2O3S/c18-14(19)5-9-3-10(4-9)7-17-15(20)12-6-11-1-2-21-13(11)8-16-12/h1-2,6,8-10H,3-5,7H2,(H,17,20)(H,18,19)/t9-,10-
• InChIKey: BFCQGZXJYIJBQN-MGCOHNPYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1csc2c1cc(nc2)C(=O)NCC3CC(C3)CC(=O)O
  CACTVS 3.385: OC(=O)C[CH]1C[CH](CNC(=O)c2cc3ccsc3cn2)C1
  CACTVS 3.385: OC(=O)C[C@@H]1C[C@@H](CNC(=O)c2cc3ccsc3cn2)C1
  ACDLabs 12.01: O=C(O)CC1CC(C1)CNC(=O)c1cc2ccsc2cn1
• Formula: C15 H16 N2 O3 S
• Name: [(1r,3r)-3-{[(thieno[2,3-c]pyridine-5-carbonyl)amino]methyl}cyclobutyl]acetic acid
• PDB chain: 5ssa Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ssa 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): D22 G48 V49 A52 G130
• Binding residue (residue number reindexed from 1): D20 G46 V47 A50 G128
• 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:5ssa, PDBe:5ssa, PDBj:5ssa
• PDBsum: 5ssa
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)