compound M1   Click here for help

GtoPdb Ligand ID: 13669

Synonyms: phenylisoxazole 4
PDB Ligand
Compound class: Synthetic organic
Comment: Compound M1 is a phenylisoxazole derivative, that was first identified as the lead for a new class of inhibitors of Arabidopsis thaliana 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD), an enzyme in the non-mevalonate (MEP) pathway of isoprenoid precursor biosynthesis [2]. It has subsequently been shown to demonstrate promising antimycobacterial activity, inhibiting Mycobacterium tuberculosis FadD32 and FadD28, members of the fatty acyl-AMP ligase family of enzymes that are essential for the biosynthesis of mycolic acids [1].
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 1
Hydrogen bond donors 1
Rotatable bonds 2
Topological polar surface area 41.82
Molecular weight 386.95
XLogP 3.71
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 C1=C(C=C(C(=C1C2=CC(=NO2)C(F)(F)F)O)Br)Br
Isomeric SMILES C1=C(C=C(C(=C1C2=CC(=NO2)C(F)(F)F)O)Br)Br
InChI InChI=1S/C10H4Br2F3NO2/c11-4-1-5(9(17)6(12)2-4)7-3-8(16-18-7)10(13,14)15/h1-3,17H
InChI Key UPPPIWMLZRPTQQ-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. Rani N, Rajmani RS, Surolia A. (2025)
Identification of an Isoxazole Derivative as an Antitubercular Compound for Targeting the FadD Enzymes of Mycobacterium tuberculosis.
J Med Chem, 68 (1): 270-286. [PMID:39693602]
2. Schwab A, Illarionov B, Frank A, Kunfermann A, Seet M, Bacher A, Witschel MC, Fischer M, Groll M, Diederich F. (2017)
Mechanism of Allosteric Inhibition of the Enzyme IspD by Three Different Classes of Ligands.
ACS Chem Biol, 12 (8): 2132-2138. [PMID:28686408]