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BDM88855   Click here for help

GtoPdb Ligand ID: 14443

PDB Ligand
Compound class: Synthetic organic
Comment: BDM88855 is a bacterial efflux pump inhibitor (EPI), discovered during medicinal chemistry efforts to optimise a series of pyridylpiperazine-based EPIs [2]. BDM88855 has potent activity against the resistance-nodulation-division (RND) family of efflux pumps of Enterobacteriaceae, binding to AcrB, the inner membrane component of the AcrAB-TolC efflux pump [2]. Further structure-based optimisation studies of this lead structure have identified BDM91288, with improved physico-chemical and pharmacokinetic properties [3], and BDM9153, with nanomolar potency [1].
EPIs have potential clinical utility as adjunctive therapeutic agents for the treatment of infections caused by Gram-negative pathogens.
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 3
Hydrogen bond donors 1
Rotatable bonds 1
Topological polar surface area 27.63
Molecular weight 247.72
XLogP 1.51
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=CC2=C(C=C1)N=C(C(=C2)Cl)N3CCNCC3
Isomeric SMILES C1CN(CCN1)C2=NC3=CC=CC=C3C=C2Cl
InChI InChI=1S/C13H14ClN3/c14-11-9-10-3-1-2-4-12(10)16-13(11)17-7-5-15-6-8-17/h1-4,9,15H,5-8H2
InChI Key JJZVQFQJCHXCFQ-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. Börnsen C, Müller RT, Vieira Da Cruz A, Jiménez-Castellanos JC, Meurillon V, Brandstätter L, Lodinsky EV, Athar M, Vargiu AV, Hartkoorn RC et al.. (2026)
Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps.
NPJ Antimicrob Resist, 4 (1). [PMID:42082832]
2. Plé C, Tam HK, Vieira Da Cruz A, Compagne N, Jiménez-Castellanos JC, Müller RT, Pradel E, Foong WE, Malloci G, Ballée A et al.. (2022)
Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps.
Nat Commun, 13 (1): 115. [PMID:35013254]
3. Vieira Da Cruz A, Jiménez-Castellanos JC, Börnsen C, Van Maele L, Compagne N, Pradel E, Müller RT, Meurillon V, Soulard D, Piveteau C et al.. (2024)
Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae.
EMBO Mol Med, 16 (1): 93-111. [PMID:38177534]