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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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Click here for structure editor
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 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

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 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

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/)
Classification Click here for help
Compound class Synthetic organic
IUPAC Name Click here for help
(2S)-N-(5-fluoro-1-hydroxypyridin-2-ylidene)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]pyrrolidine-2-carboxamide
Synonyms Click here for help
LBM415 | NVP LBM-415 | NVP-PDF-713 | PDF-713 | VIC-104959
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo VIC-104959
Other databases
CAS Registry No. 478913-91-6 (source: ChemIDplus)
ChEMBL Ligand CHEMBL221667
GtoPdb PubChem SID 405560484
PubChem CID 9690139
Search Google for chemical match using the InChIKey AYCMYBACERJYNY-HIFRSBDPSA-N
Search Google for chemicals with the same backbone AYCMYBACERJYNY
UniChem Compound Search for chemical match using the InChIKey AYCMYBACERJYNY-HIFRSBDPSA-N
UniChem Connectivity Search for chemical match using the InChIKey AYCMYBACERJYNY-HIFRSBDPSA-N