paromomycin   Click here for help

GtoPdb Ligand ID: 12160

Synonyms: aminosidine | catenulin | Humatin® | monomycin A
Approved drug PDB Ligand
paromomycin is an approved drug (FDA (1969))
Compound class: Natural product
Comment: Paromomycin belongs to the aminoglycoside class of antibacterial compounds and was originally isolated from Streptomyces krestomuceticus. It is used as an antiprotozoal drug and is included in the World Health Organization's Model List of Essential Medicines (link provided in the Classification table, under the Summary tab below).
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 19
Hydrogen bond donors 13
Rotatable bonds 9
Topological polar surface area 347.32
Molecular weight 615.3
XLogP -6.85
No. Lipinski's rules broken 2

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 OC[C@H]1O[C@H]([C@@H]([C@@H]1O[C@H]1O[C@@H](CN)[C@H]([C@@H]([C@H]1N)O)O)O)O[C@@H]1[C@@H](O)[C@H](N)C[C@@H]([C@H]1O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1N)O)O)N
Isomeric SMILES C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)N)O[C@H]1[C@@H]([C@@H]([C@H](O1)CO)O[C@@H]1[C@@H]([C@H]([C@@H]([C@@H](O1)CN)O)O)N)O)O)N
InChI InChI=1S/C23H45N5O14/c24-2-7-13(32)15(34)10(27)21(37-7)41-19-9(4-30)39-23(17(19)36)42-20-12(31)5(25)1-6(26)18(20)40-22-11(28)16(35)14(33)8(3-29)38-22/h5-23,29-36H,1-4,24-28H2/t5-,6+,7+,8-,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1
InChI Key UOZODPSAJZTQNH-LSWIJEOBSA-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. Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. (2000)
Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics.
Nature, 407 (6802): 340-8. [PMID:11014183]
2. Davidson RN, den Boer M, Ritmeijer K. (2009)
Paromomycin.
Trans R Soc Trop Med Hyg, 103 (7): 653-60. [PMID:18947845]