amikacin   Click here for help

GtoPdb Ligand ID: 10894

Synonyms: Amikin® | AMK | Arikayce liposomal® | BB-K8
Approved drug PDB Ligand
amikacin is an approved drug (FDA (1981), EMA (2020))
Compound class: Synthetic organic
Comment: Amikacin is a semi-synthetic aminoglycoside antibacterial that is active against a broad spectrum of Gram-negative organisms, including pseudomonas and some Gram-positive organisms (principally Staphylococcus aureus, including some methicillin-resistant strains). It is a kanamycin derivative. Functionally it binds to the bacterial 30S ribosomal subunit and disrupts protein synthesis, thereby creating its bactericidal effect.
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 18
Hydrogen bond donors 13
Rotatable bonds 11
Topological polar surface area 331.94
Molecular weight 585.29
XLogP -6.56
No. Lipinski's rules broken 2
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 NCC[C@@H](C(=O)N[C@@H]1C[C@H](N)[C@H]([C@@H]([C@H]1O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)N)O)O)O[C@H]1O[C@H](CN)[C@H]([C@@H]([C@H]1O)O)O)O
Isomeric SMILES NCC[C@@H](C(=O)N[C@@H]1C[C@H](N)[C@H]([C@@H]([C@H]1O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)N)O)O)O[C@H]1O[C@H](CN)[C@H]([C@@H]([C@H]1O)O)O)O
InChI InChI=1S/C22H43N5O13/c23-2-1-8(29)20(36)27-7-3-6(25)18(39-22-16(34)15(33)13(31)9(4-24)37-22)17(35)19(7)40-21-14(32)11(26)12(30)10(5-28)38-21/h6-19,21-22,28-35H,1-5,23-26H2,(H,27,36)/t6-,7+,8-,9+,10+,11-,12+,13+,14+,15-,16+,17-,18+,19-,21+,22+/m0/s1
InChI Key LKCWBDHBTVXHDL-RMDFUYIESA-N
References
1. Li CR, Yang XY, Lou RH, Zhang WX, Wang YM, Yuan M, Li Y, Chen HZ, Hong B, Sun CH et al.. (2008)
In vitro antibacterial activity of vertilmicin and its susceptibility to modifications by the recombinant AAC6'-APH2'' enzyme.
Antimicrob Agents Chemother, 52 (11): 3875-82. [PMID:18710917]