hygromycin A   Click here for help

GtoPdb Ligand ID: 13623

Synonyms: homomycin | totomycin
Compound class: Natural product
Comment: Hygromycin A is an antibacterial compound, isolated from Streptomyces hygroscopicus and first identified in 1953. It has recently been shown to have selective activity against spirochaetes, including Borrelia burgdorferi a species that causes Lyme disease [2].

hygromycin A is commercially available from our sponsors

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 13
Hydrogen bond donors 7
Rotatable bonds 7
Topological polar surface area 204.47
Molecular weight 511.48
XLogP -1.76
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 C/C(=C\C1=CC=C(C(=C1)O)O[C@H]2[C@H]([C@@H]([C@@H](C(=O)C)O2)O)O)/C(=O)N[C@@H]3[C@@H]([C@H]([C@@H]4[C@H]([C@@H]3O)OCO4)O)O
Isomeric SMILES C/C(=C\C1=CC(=C(C=C1)O[C@H]2[C@H]([C@@H]([C@H](O2)C(=O)C)O)O)O)/C(=O)N[C@@H]3[C@@H]([C@H]([C@@H]4[C@H]([C@@H]3O)OCO4)O)O
InChI InChI=1S/C23H29NO12/c1-8(22(32)24-13-14(27)16(29)21-20(15(13)28)33-7-34-21)5-10-3-4-12(11(26)6-10)35-23-18(31)17(30)19(36-23)9(2)25/h3-6,13-21,23,26-31H,7H2,1-2H3,(H,24,32)/b8-5+/t13-,14+,15-,16-,17+,18+,19-,20+,21-,23-/m1/s1
InChI Key YQYJSBFKSSDGFO-IIHALWDASA-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/)
No information available.
Mechanism Of Action and Pharmacodynamic Effects Click here for help
Hygromycin A binds to the peptidyl transferase center (PTC) of the bacterial 50S ribosomal subunit, leading to inhibition of peptide bond formation [1]. The compound is selectively taken up by spirochaetes via BmpDEFG, a BmpD nucleoside transporter essential to this class of bacteria [2].