GtoPdb is requesting financial support from commercial users. Please see our sustainability page for more information.

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.

amikacin is commercially available from our sponsors

2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

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.

✖
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

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
Click here for help

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/)

✖
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

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
Approved drug? Yes. EU EMA (2020)  |  US FDA (1981)
WHO Essential Medicine WHO Essential Medicines List (EML) (23rd List, 2023). Access PDF version.
Click to view more information about the WHO Model Lists of Essential Medicines.
IUPAC Name Click here for help
(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-2-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-trihydroxyoxan-2-yl]oxy-3-hydroxycyclohexyl]-2-hydroxybutanamide
International Nonproprietary Names Click here for help
INN number INN
3492 amikacin
Synonyms Click here for help
Amikin® | AMK | Arikayce liposomal® | BB-K8
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Amikacin
Other databases
BindingDB Ligand 50237603
CAS Registry No. 37517-28-5 (source: WHO INN record)
ChEMBL Ligand CHEMBL177
DrugBank Ligand DB00479
DrugCentral Ligand 157
GtoPdb PubChem SID 405560335
PubChem CID 37768
RCSB PDB Ligand AKN
Search Google for chemical match using the InChIKey LKCWBDHBTVXHDL-RMDFUYIESA-N
Search Google for chemicals with the same backbone LKCWBDHBTVXHDL
Search PubMed clinical trials amikacin
Search PubMed titles amikacin
Search PubMed titles/abstracts amikacin
UniChem Compound Search for chemical match using the InChIKey LKCWBDHBTVXHDL-RMDFUYIESA-N
UniChem Connectivity Search for chemical match using the InChIKey LKCWBDHBTVXHDL-RMDFUYIESA-N

Product suppliers

View disclaimer

Sponsored products disclaimer

Product supplier links are provided as a service to assist in identifying commercial suppliers of reagents that are mentioned on the IUPHAR/BPS Guide to PHARMACOLOGY database website, and do not imply their endorsement by NC-IUPHAR.

Links are provided in return for sponsorship, used to fund improvements to this database. The sponsorship account is managed and audited by the University of Edinburgh, a charitable body registered in Scotland, SC005336. If you are interested in sponsoring the database, please contact us.

✖

MedChemExpress
Amikacin (links to external site)
Cat. No. HY-B0509A