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iboxamycin   Click here for help

GtoPdb Ligand ID: 11790

Synonyms: IBX | OPP-3
Compound class: Synthetic organic
Comment: Iboxamycin (OPP-3) is an orally bioavailable, synthetic antibacterial compound, discovered through a collaboration between the University of Illinois at Chicago and Harvard University [1]. Structurally, IBX is built on a oxepanoproline scaffold that is linked to the aminooctose residue of clindamycin. X-ray crystallography shows that IBX binds to the large ribosomal subunit in the bacteria (more effectively than clindamycin) and disrupts translation initiation. Iboxamycin is a novel broad-spectrum agent that is active against Gram-positive and Gram-negative bacteria including ESKAPE pathogens that express resistance-conferring Erm and Cfr ribosomal RNA methyltransferase enzymes.
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 8
Hydrogen bond donors 5
Rotatable bonds 8
Topological polar surface area 145.58
Molecular weight 494.22
XLogP 2.71
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 CSC1O[C@@H]([C@@H]([C@@H](Cl)C)NC(=O)[C@H]2NC[C@H]3[C@H]2OCC[C@H](C3)CC(C)C)C([C@H]([C@H]1O)O)O
Isomeric SMILES [C@H]12CN[C@H](C(=O)N[C@H]([C@H](C)Cl)[C@@H]3OC(SC)[C@H](O)[C@H](O)C3O)[C@@H]1OCC[C@@H](CC(C)C)C2
InChI InChI=1S/C22H39ClN2O6S/c1-10(2)7-12-5-6-30-19-13(8-12)9-24-15(19)21(29)25-14(11(3)23)20-17(27)16(26)18(28)22(31-20)32-4/h10-20,22,24,26-28H,5-9H2,1-4H3,(H,25,29)/t11-,12-,13-,14+,15-,16+,17?,18+,19+,20-,22?/m0/s1
InChI Key JPCLUJPDWMBCAA-ALYUFWCISA-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
(4S,5aS,8S,8aR)-N-[(1S,2S)-2-chloro-1-[(2S,4R,5R)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-4-(2-methylpropyl)-octahydro-2H-oxepino[2,3-c]pyrrole-8-carboxamide
Synonyms Click here for help
IBX | OPP-3
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Iboxamycin
Other databases
GtoPdb PubChem SID 458923825
PubChem CID 162366972
Search Google for chemical match using the InChIKey JPCLUJPDWMBCAA-ALYUFWCISA-N
Search Google for chemicals with the same backbone JPCLUJPDWMBCAA
UniChem Compound Search for chemical match using the InChIKey JPCLUJPDWMBCAA-ALYUFWCISA-N
UniChem Connectivity Search for chemical match using the InChIKey JPCLUJPDWMBCAA-ALYUFWCISA-N