JEDI-852   Click here for help

GtoPdb Ligand ID: 13332

PDB Ligand
Compound class: Synthetic organic
Comment: JEDI-852 is the hit molecule from a series of antibacterial compounds that target UDP-2,3-diacylglucosamine hydrolase (LpxH), an enzyme in the lipopolysaccharide synthesis pathway [1]. LpxH is an essential enzyme, conserved in the majority of Gram-negative bacteria but absent in human.
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 8
Hydrogen bond donors 1
Rotatable bonds 7
Topological polar surface area 120.62
Molecular weight 451.56
XLogP 1.07
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
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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)N3CCCCC3)S(=O)(=O)C
Isomeric SMILES CN(C1=C(C=CC=C1)C(=O)NC2=CC=C(C=C2)S(=O)(=O)N3CCCCC3)S(C)(=O)=O
InChI InChI=1S/C20H25N3O5S2/c1-22(29(2,25)26)19-9-5-4-8-18(19)20(24)21-16-10-12-17(13-11-16)30(27,28)23-14-6-3-7-15-23/h4-5,8-13H,3,6-7,14-15H2,1-2H3,(H,21,24)
InChI Key WMMQKHOYQUOGHM-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/)
References
1. Huseby DL, Cao S, Zamaratski E, Sooriyaarachchi S, Ahmad S, Bergfors T, Krasnova L, Pelss J, Ikaunieks M, Loza E et al.. (2024)
Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.
Proc Natl Acad Sci U S A, 121 (15): e2317274121. [PMID:38579010]