LBM-415   Click here for help

GtoPdb Ligand ID: 11043

Synonyms: LBM415 | NVP LBM-415 | NVP-PDF-713 | PDF-713 | VIC-104959
Compound class: Synthetic organic
Comment: LBM-415 is an antibacterial that acts as a peptide deformylase (PDF) inhibitor [4]. It has in vitro activity against pathogenic staphylococci and enterococci, including respiratory tract pathogens such as Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis [1-2,5].
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 CDK toolkit. 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 5
Hydrogen bond donors 2
Rotatable bonds 10
Topological polar surface area 115.44
Molecular weight 396.18
XLogP 1.39
No. Lipinski's rules broken 0
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.

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Canonical SMILES CCCC[C@@H](C(=O)N1CCC[C@H]1C(=O)N=c1ccc(cn1O)F)CN(C=O)O
Isomeric SMILES CCCC[C@@H](C(=O)N1CCC[C@H]1C(=O)N=c1ccc(cn1O)F)CN(C=O)O
InChI InChI=1S/C18H25FN4O5/c1-2-3-5-13(10-21(27)12-24)18(26)22-9-4-6-15(22)17(25)20-16-8-7-14(19)11-23(16)28/h7-8,11-13,15,27-28H,2-6,9-10H2,1H3/t13-,15+/m1/s1
InChI Key AYCMYBACERJYNY-HIFRSBDPSA-N
References
1. Anderegg TR, Jones RN, Quality Control Working Group. (2004)
Disk diffusion quality control guidelines for NVP-PDF 713: a novel peptide deformylase inhibitor.
Diagn Microbiol Infect Dis, 48 (1): 55-7. [PMID:14761722]
2. Jones RN, Moet GJ, Sader HS, Fritsche TR. (2004)
Potential utility of a peptide deformylase inhibitor (NVP PDF-713) against oxazolidinone-resistant or streptogramin-resistant Gram-positive organism isolates.
J Antimicrob Chemother, 53 (5): 804-7. [PMID:15056649]
3. Kosowska-Shick K, Credito KL, Pankuch GA, DeWasse B, McGhee P, Appelbaum PC. (2007)
Multistep resistance selection and postantibiotic-effect studies of the antipneumococcal activity of LBM415 compared to other agents.
Antimicrob Agents Chemother, 51 (2): 770-3. [PMID:17116666]
4. Sangshetti JN, Khan FA, Shinde DB. (2015)
Peptide deformylase: a new target in antibacterial, antimalarial and anticancer drug discovery.
Curr Med Chem, 22 (2): 214-36. [PMID:25174923]
5. Waites KB, Reddy NB, Crabb DM, Duffy LB. (2005)
Comparative in vitro activities of investigational peptide deformylase inhibitor NVP LBM-415 and other agents against human mycoplasmas and ureaplasmas.
Antimicrob Agents Chemother, 49 (6): 2541-2. [PMID:15917568]