compound 3k [PMID: 24568342]   Click here for help

GtoPdb Ligand ID: 10748

PDB Ligand
Compound class: Synthetic organic
Comment: Compound 3k is reported as an inhibitor of the papain-like protease (PL-pro) of SARS-CoV [1]. It was the most potent in the series both in terms of inhibiting enzyme activity (IC50 150 nM) and in terms of reducung viral replication in cell culture (EC50 = 5400 nM). The X-ray structure of the PL-pro/3k complex was submitted to the RCSB Protein Data Bank and has accession 4OW0. Activity of 3k vs. SARS-CoV-2 PL-pro has not yet been published.
2D Structure
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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.

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Physico-chemical Properties
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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.

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Hydrogen bond acceptors 3
Hydrogen bond donors 1
Rotatable bonds 6
Topological polar surface area 32.34
Molecular weight 390.21
XLogP 5.14
No. Lipinski's rules broken 1

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
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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/)

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Canonical SMILES Fc1cccc(c1)CNC(=O)C1CCN(CC1)[C@@H](c1cccc2c1cccc2)C
Isomeric SMILES Fc1cccc(c1)CNC(=O)C1CCN(CC1)[C@@H](c1cccc2c1cccc2)C
InChI InChI=1S/C25H27FN2O/c1-18(23-11-5-8-20-7-2-3-10-24(20)23)28-14-12-21(13-15-28)25(29)27-17-19-6-4-9-22(26)16-19/h2-11,16,18,21H,12-15,17H2,1H3,(H,27,29)/t18-/m1/s1
InChI Key XJTWGMHOQKGBDO-GOSISDBHSA-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/)
References
1. Báez-Santos YM, Barraza SJ, Wilson MW, Agius MP, Mielech AM, Davis NM, Baker SC, Larsen SD, Mesecar AD. (2014)
X-ray structural and biological evaluation of a series of potent and highly selective inhibitors of human coronavirus papain-like proteases.
J Med Chem, 57 (6): 2393-412. [PMID:24568342]