PRD_002214   Click here for help

GtoPdb Ligand ID: 10716

Compound class: Synthetic organic
Comment: PRD_002214 is an irreversible peptide-like inhibitor of the main protease (MPRO) of SARS-CoV-2 [1]. The chemical structure was obtained from the RCSB Protein Data Bank entry 6LU7 which shows the ligand in complex with the protease. The article describing the work has not yet been published (March 12, 2020), but the inhibitor (also referred to as N3) has been deployed in other MPRO crystallisation studies [2]. The MPRO sequence is held in the NCBI record 'Chain A, SARS-CoV-2 main protease'.
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2D Structure
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Physico-chemical Properties
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Hydrogen bond acceptors 12
Hydrogen bond donors 5
Rotatable bonds 22
Topological polar surface area 197.83
Molecular weight 680.35
XLogP 3.31
No. Lipinski's rules broken 2
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Canonical SMILES CC(C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)/C=C\C(=O)OCc1ccccc1)NC(=O)[C@H](C(C)C)NC(=O)[C@@H](NC(=O)c1noc(c1)C)C)C
Isomeric SMILES CC(C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)/C=C\C(=O)OCc1ccccc1)NC(=O)[C@H](C(C)C)NC(=O)[C@@H](NC(=O)c1noc(c1)C)C)C
InChI InChI=1S/C35H48N6O8/c1-20(2)16-27(39-35(47)30(21(3)4)40-31(43)23(6)37-34(46)28-17-22(5)49-41-28)33(45)38-26(18-25-14-15-36-32(25)44)12-13-29(42)48-19-24-10-8-7-9-11-24/h7-13,17,20-21,23,25-27,30H,14-16,18-19H2,1-6H3,(H,36,44)(H,37,46)(H,38,45)(H,39,47)(H,40,43)/b13-12-/t23-,25-,26+,27-,30-/m0/s1
Bioactivity Comments
PRD_002214 inhibits hCoV-229E MPRO with a Ki of 1.67 μM, and SARS-CoV MPROwith a Ki of 9 μM in vitro [2]. hCoV-229E replication is inhibited by PRD_002214 (IC50 4 μM). A dissociation constant (Ki) for the PRD_002214 interaction with SARS-CoV-2 MPRO could not be determined because of its very potent, irreversible and rapid interaction [1].
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
CoV 3C-like (main) protease SARS-CoV Inhibitor Inhibition 5.1 pIC50 - 2
pIC50 5.1 (IC50 9x10-6 M) [2]
CoV 3C-like (main) protease SARS-CoV-2 Inhibitor Irreversible inhibition - - - 1