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JEDI-1444   Click here for help

GtoPdb Ligand ID: 14227

PDB Ligand
Compound class: Synthetic organic
Comment: JEDI-1444 is from a series of antibacterial compounds that target UDP-2,3-diacylglucosamine hydrolase (LpxH), an essential enzyme in the lipopolysaccharide synthesis pathway, that is conserved in the majority of Gram-negative bacteria but absent in human [1]. JEDI-1444 was identified as part of a programme to develop LpxH inhibitors with activity against efflux-proficient Gram-negative bacteria. It was designed by combining structural elements from existing LpxH inhibitors AZ1 and JEDI-852 and was subsequently used to derive improved analogues EBL-3599 and EBL-3647.
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 9
Hydrogen bond donors 1
Rotatable bonds 9
Topological polar surface area 123.86
Molecular weight 596.64
XLogP 2.14
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 CN(C1=C(C=CC=C1)C(=O)NC2=CC=C(C=C2)S(=O)(=O)N3CCN(CC3)C4=CC(=CC=C4)C(F)(F)F)S(=O)(=O)C
Isomeric SMILES CN(C1=CC=CC=C1C(=O)NC2=CC=C(C=C2)S(=O)(=O)N3CCN(CC3)C4=CC=CC(=C4)C(F)(F)F)S(=O)(=O)C
InChI InChI=1S/C26H27F3N4O5S2/c1-31(39(2,35)36)24-9-4-3-8-23(24)25(34)30-20-10-12-22(13-11-20)40(37,38)33-16-14-32(15-17-33)21-7-5-6-19(18-21)26(27,28)29/h3-13,18H,14-17H2,1-2H3,(H,30,34)
InChI Key JURGWQSEARSCQN-UHFFFAOYSA-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
JEDI-1444 exhibits Gram-negative antibacterial activity and is effective against efflux-proficient strains of Escherichia coli and Klebsiella pneumoniae [1]. However, it has weak antibacterial activity in the presence of serum and is also limited by low solubility and poor metabolic stability.
JEDI-1444 inhibits E.coli LpxH with an IC50 of 2.6 nM [1].