LPC-233   Click here for help

GtoPdb Ligand ID: 13824

PDB Ligand
Compound class: Synthetic organic
Comment: LPC-233 is an orally bioavailable preclinical antibacterial compound that inhibits bacterial UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) and has potent activity against a wide range of Gram-negative bacteria in vitro [5].
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 4
Hydrogen bond donors 4
Rotatable bonds 7
Topological polar surface area 98.66
Molecular weight 376.35
XLogP 2.57
No. Lipinski's rules broken 0

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 C[C@]([C@@H](C(=O)NO)NC(=O)C1=CC=C(C#CC#CC2CC2)C=C1)(C(F)F)O
Isomeric SMILES C[C@]([C@@H](C(=O)NO)NC(=O)C1=CC=C(C=C1)C#CC#CC2CC2)(C(F)F)O
InChI InChI=1S/C19H18F2N2O4/c1-19(26,18(20)21)15(17(25)23-27)22-16(24)14-10-8-13(9-11-14)5-3-2-4-12-6-7-12/h8-12,15,18,26-27H,6-7H2,1H3,(H,22,24)(H,23,25)/t15-,19+/m1/s1
InChI Key NPTNDHDCCLLFJE-BEFAXECRSA-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. Erwin AL. (2016)
Antibacterial Drug Discovery Targeting the Lipopolysaccharide Biosynthetic Enzyme LpxC.
Cold Spring Harb Perspect Med, 6 (7). [PMID:27235477]
2. Niu Z, Lei P, Wang Y, Wang J, Yang J, Zhang J. (2023)
Small molecule LpxC inhibitors against gram-negative bacteria: Advances and future perspectives.
Eur J Med Chem, 253: 115326. [PMID:37023679]
3. Raetz CR. (1993)
Bacterial endotoxins: extraordinary lipids that activate eucaryotic signal transduction.
J Bacteriol, 175 (18): 5745-53. [PMID:8376321]
4. Raetz CR, Guan Z, Ingram BO, Six DA, Song F, Wang X, Zhao J. (2009)
Discovery of new biosynthetic pathways: the lipid A story.
J Lipid Res, 50 Suppl (Suppl): S103-8. [PMID:18974037]
5. Zhao J, Cochrane CS, Najeeb J, Gooden D, Sciandra C, Fan P, Lemaitre N, Newns K, Nicholas RA, Guan Z et al.. (2023)
Preclinical safety and efficacy characterization of an LpxC inhibitor against Gram-negative pathogens.
Sci Transl Med, 15 (708): eadf5668. [PMID:37556556]