PRD_002214   

GtoPdb Ligand ID: 10716

Synonyms: inhibitor N3 | N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
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'.
2D Structure
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Physico-chemical Properties
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
SMILES / InChI / InChIKey
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
InChI Key IDBWWEGDLCFCTD-NQJFWITJSA-N
Classification
Compound class Synthetic organic
IUPAC Name
benzyl (2Z,4S)-4-[(2S)-4-methyl-2-[(2S)-3-methyl-2-[(2S)-2-[(5-methyl-1,2-oxazol-3-yl)formamido]propanamido]butanamido]pentanamido]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
Synonyms
inhibitor N3 | N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
Database Links
GtoPdb PubChem SID 405067310
RCSB PDB Ligand PRD_002214
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