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TP0586532   Click here for help

GtoPdb Ligand ID: 14296

PDB Ligand
Compound class: Synthetic organic
Comment: TP0586532 is a non-hydroxamate inhibitor of bacterial UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) [6]. LpxC is an attractive target for the development of antibacterial agents against Gram-negative bacterial pathogens, although safety and activity issues have so far precluded approval for clinical use of these drugs [1,3]. LpxC inhibitors that do not contain a hydroxamate moiety, such as TP0586532, are predicted to have a reduced risk of cardiovascular toxicity.
Note that the structure shown here matches the CAS-assigned structure. The PubChem link, provided in the table below, is to their standardized chemical structure (CID 155294517), although this is not an exact structural match.
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 6
Hydrogen bond donors 2
Rotatable bonds 8
Topological polar surface area 97.96
Molecular weight 460.53
XLogP 1.98
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 C[C@@H](C1=NC=CN1CC2=NOC(=C2)C3=CC=C(C=C3)C#C[C@H]4[C@]5([H])CN(CCCC(=O)O)C[C@]45[H])O
Isomeric SMILES C(#CC1=CC=C(C=C1)C2=CC(CN3C([C@H](C)O)=NC=C3)=NO2)[C@H]4[C@]5([C@@]4(CN(CCCC(O)=O)C5)[H])[H]
InChI InChI=1S/C26H28N4O4/c1-17(31)26-27-10-12-30(26)14-20-13-24(34-28-20)19-7-4-18(5-8-19)6-9-21-22-15-29(16-23(21)22)11-2-3-25(32)33/h4-5,7-8,10,12-13,17,21-23,31H,2-3,11,14-16H2,1H3,(H,32,33)/t17-,21-,22-,23+/m0/s1
InChI Key PULUMLQUYYSBOR-KEIZBESESA-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. Fujita K, Takata I, Yoshida I, Okumura H, Otake K, Takashima H, Sugiyama H. (2022)
TP0586532, a non-hydroxamate LpxC inhibitor, has in vitro and in vivo antibacterial activities against Enterobacteriaceae.
J Antibiot (Tokyo), 75 (2): 98-107. [PMID:34837061]
3. 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]
4. Raetz CR. (1993)
Bacterial endotoxins: extraordinary lipids that activate eucaryotic signal transduction.
J Bacteriol, 175 (18): 5745-53. [PMID:8376321]
5. 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]
6. Ushiyama F, Takashima H, Matsuda Y, Ogata Y, Sasamoto N, Kurimoto-Tsuruta R, Ueki K, Tanaka-Yamamoto N, Endo M, Mima M et al.. (2021)
Lead optimization of 2-hydroxymethyl imidazoles as non-hydroxamate LpxC inhibitors: Discovery of TP0586532.
Bioorg Med Chem, 30: 115964. [PMID:33385955]