GtoPdb is requesting financial support from commercial users. Please see our sustainability page for more information.

example 2 [WO2005113580A1]   Click here for help

GtoPdb Ligand ID: 11106

PDB Ligand
Compound class: Synthetic organic
Comment: Example 2 is a covalent inhibitor of the 3CL protease (Mpro) of the SARS-CoV-1 coronavirus [1]. The compound has been shown in complex with SARS-CoV-2 Mpro (see RCSB Protein Database entry 6XHM).
2D Structure
Click here for help

2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

✖
Hydrogen bond acceptors 8
Hydrogen bond donors 6
Rotatable bonds 13
Topological polar surface area 152.78
Molecular weight 474.25
XLogP 1
No. Lipinski's rules broken 2

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
Click here for help

SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

✖
Canonical SMILES OC[C@H]([C@@H](NC(=O)[C@@H](NC(=O)c1[nH]c2c(c1)c(OC)ccc2)CC(C)C)C[C@@H]1CCNC1=O)O
Isomeric SMILES OC[C@H]([C@@H](NC(=O)[C@@H](NC(=O)c1[nH]c2c(c1)c(OC)ccc2)CC(C)C)C[C@@H]1CCNC1=O)O
InChI InChI=1S/C24H34N4O6/c1-13(2)9-18(23(32)27-17(20(30)12-29)10-14-7-8-25-22(14)31)28-24(33)19-11-15-16(26-19)5-4-6-21(15)34-3/h4-6,11,13-14,17-18,20,26,29-30H,7-10,12H2,1-3H3,(H,25,31)(H,27,32)(H,28,33)/t14-,17-,18-,20+/m0/s1
InChI Key FDQSUXUTXIGUIA-PRIDNEQBSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Bioactivity Comments
Example 2 inhibits 3CL protease (Mpro) of the SARS-CoV-1 coronavirus with an IC50 of 4 nM (in a FRET assay measuring protease catalysed cleavage of a TAMRA-labelled substrate peptide) and has in vitro antiviral activity [1].