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cerastecin D   Click here for help

GtoPdb Ligand ID: 14290

Compound class: Synthetic organic
Comment: Cerastecin D is the lead from a novel class of antibacterial compounds that have activity against Acinetobacter baumannii [2]. The structure is claimed in Merck's patent WO2023224893A1 [1]. Functionally it inhibits MsbA, a lipooligosaccharide (LOS) ATP-binding cassette (ABC) transporter that is essential in A. baumannii [3].
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 16
Hydrogen bond donors 4
Rotatable bonds 14
Topological polar surface area 227.37
Molecular weight 805.79
XLogP 1.82
No. Lipinski's rules broken 3

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(=C1)NS(=O)(=O)C2=CN(C3=CC=C(C=C3)F)N=C2)C(=O)O)CN4CC(C4)OC5=CC=C(C(=C5)C(=O)O)NS(=O)(=O)C6=CN(C7=CC=C(C=C7)F)N=C6
Isomeric SMILES O=S(NC=1C(C(O)=O)=CC(=CC1)CN2CC(OC3=CC(C(O)=O)=C(NS(=O)(C4=CN(C5=CC=C(F)C=C5)N=C4)=O)C=C3)C2)(C6=CN(C7=CC=C(F)C=C7)N=C6)=O
InChI InChI=1S/C36H29F2N7O9S2/c37-23-2-6-25(7-3-23)44-20-29(15-39-44)55(50,51)41-33-11-1-22(13-31(33)35(46)47)17-43-18-28(19-43)54-27-10-12-34(32(14-27)36(48)49)42-56(52,53)30-16-40-45(21-30)26-8-4-24(38)5-9-26/h1-16,20-21,28,41-42H,17-19H2,(H,46,47)(H,48,49)
InChI Key KWLPOBODVPIQQW-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. Raheem I, Balibar CJ, Skudlarek JW, Labroli MA, Mitchell H, Tong L, Forster A, Hunter DN, Li SW, Wang H et al.. (2023)
Inhibitors of msba as antibiotics, pharmaceutical compositions, and uses thereof.
Patent number: WO2023224893A1. Assignee: Merck Sharp and Dohme LLC. Priority date: 15/05/2023. Publication date: 23/11/2023.
2. Skudlarek JW, Cooke AJ, Mitchell HJ, Babaoglu K, Shaw AW, Tong L, Nomland AB, Labroli M, Sha D, Mulhearn JJ et al.. (2024)
Cerastecin Inhibition of the Lipooligosaccharide Transporter MsbA to Combat Acinetobacter baumannii: From Screening Impurity to In Vivo Efficacy.
J Med Chem, 67 (17): 15620-15675. [PMID:39172133]
3. Wang H, Ishchenko A, Skudlarek J, Shen P, Dzhekieva L, Painter RE, Chen YT, Bukhtiyarova M, Leithead A, Tracy R et al.. (2024)
Cerastecins inhibit membrane lipooligosaccharide transport in drug-resistant Acinetobacter baumannii.
Nat Microbiol, 9 (5): 1244-1255. [PMID:38649414]