Amikacin

Athanor · official

C₂₂H₄₃N₅O₁₃ · 585.6 g/mol

IUPAC name: (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

Also called Amikin, aminoglycoside, kanamycin derivative

Drugs

Open in Athanor

Drawn from its SMILES with RDKit

DangerMay cause an allergic skin reaction · Causes serious eye damage · Harmful if inhaled · May damage fertility or the unborn child · Causes damage to organs through prolonged or repeated exposure

Names and identifiers

IUPAC name: (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
Synonyms: Amikin, aminoglycoside, kanamycin derivative
+ 38 more
Lukadin, amikacine, Amikacina, Amikacinum, Potentox, 1-N-(L(-)-gamma-Amino-alpha-hydroxybutyryl)kanamycin A, DTXSID3022586, BAY 41-6551, CHEBI:2637, (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, 84319SGC3C, NSC-177001, DTXCID002586, (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, D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1->6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1->4))-N(sup 1)-(4-amino-2-hydroxy-1-oxobutyl)-2-deoxy-, (S)-, D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1-6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1-4))-N1-(4-amino-2-hydroxy-1-oxobutyl)-2-deoxy-, (S)-, Amiklin, D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1.fwdarw.6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1.fwdarw.4))-N1-((2S)-4-amino-2-hydroxy-1-oxobutyl)-2-deoxy-, Biclin, Normon, Amikacina, Medical, Amikacina, (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, (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, RefChem:5541, D06AX12, J01GB06, S01AA21, 253-538-5, O-3-AMINO-3-DEOXY-alpha-D-GLUCOPYRANOSYL-(1->4)-O-(6-AMINO-6-DEOXY-alpha-D-GLUCOPYRANOSYL-(1->6))-N(SUP 3)-(4-AMINO-L-2-HYDROXYBUTYRYL)-2-DEOXY-L-STREPTAMINE, Amikacillin, Amikacine [INN-French], Amikacinum [INN-Latin], Amikacina [INN-Spanish], Amikacin Base, Kaminax, Amikacin Dihydrate, Amicacin, Briclin
Molecular formula: C₂₂H₄₃N₅O₁₃
Empirical formula: C₂₂H₄₃N₅O₁₃
Molecular weight: 585.6 g/mol
Exact mass: 585.28574
CAS number: 37517-28-5
PubChem CID: 37768
Canonical SMILES: C1C(C(C(C(C1NC(=O)C(CCN)O)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(C(C(C(O3)CN)O)O)O)N
Isomeric SMILES: C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](CCN)O)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)O)N
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
InChIKey: LKCWBDHBTVXHDL-RMDFUYIESA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Physical properties

Solubility in water: In water, 1.85 × 10⁵ mg/L at 25 °C[1]
pKa: pKa1 = 6.7 (primary amine)[1]
4 values
Only one source reports it.
Value As written Source
–shown pKa1 = 6.7 (primary amine) [1] Hazardous Substances Data Bank (HSDB)cites Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
– pKa2 = 8.4 (primary amine) [1] Hazardous Substances Data Bank (HSDB)cites Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
– pKa3 = 8.4 (primary amine) [1] Hazardous Substances Data Bank (HSDB)cites Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
– pKa4 = 9.7 (primary amine) [1] Hazardous Substances Data Bank (HSDB)cites Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)

Value	As written	Source
–shown	pKa1 = 6.7 (primary amine)	[1] Hazardous Substances Data Bank (HSDB)cites Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
–	pKa2 = 8.4 (primary amine)	[1] Hazardous Substances Data Bank (HSDB)cites Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
–	pKa3 = 8.4 (primary amine)	[1] Hazardous Substances Data Bank (HSDB)cites Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
–	pKa4 = 9.7 (primary amine)	[1] Hazardous Substances Data Bank (HSDB)cites Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)

Each value as its source reports it, with the source's number after it (listed under References). Where several sources report a property, the row shows the value most of them agree on, the rule the app uses; open the values to see every one.

Calculated

Heavy atoms: 40
Rings: 3
Aromatic rings: 0
Fraction sp³ carbons (Fsp3): 0.95
H-bond donors: 13
H-bond acceptors: 17
Rotatable bonds: 10
TPSA (Å²): 331.9 computed here · PubChem 332
Formal charge: 0
XLogP3: -7.9 PubChem
Complexity: 819 PubChem
Stereocenters: 16 definedCIP: C4: S · C9: R · C11: S · C13: R · C15: S · C17: R · C20: S · C22: R · C24: R · C26: S · C28: S · C30: R
Double-bond geometry: None specified
Point group: C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

C45.12%
H7.40%
N11.96%
O35.52%

Isotope pattern

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P: -8.42 Crippen (Wildman and Crippen 1999)
log S (water solubility): 2.5 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 5.27 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 585.61
log P ≤ 5 (Crippen): -8.42
H-bond donors ≤ 5: 13
H-bond acceptors ≤ 10: 17

Breaks 3 of the four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

Danger

Most widely reported: 4 company reports to ECHA. Source [2].

Corrosive
Harmful or irritant
Health hazard

H317May cause an allergic skin reaction (75% of reports)
H318Causes serious eye damage (25% of reports)
H332Harmful if inhaled (25% of reports)
H360May damage fertility or the unborn child (25% of reports)
H372Causes damage to organs through prolonged or repeated exposure (25% of reports)

Precautionary statements: P203, P260, P261, P264, P264+P265, P270, P271, P272, P280, P302+P352, P304+P340, P305+P354+P338, P317, P318, P319, P321, P333+P317, P362+P364, P405, P501

Storage

Store at 20 deg to 25 °C (68 deg to 77 °F); excursions permitted between 15 deg to 30 °C (59 deg to 86 °F)[1]

Safety data sheets on the supplier’s page: AbaChemScene, Enamine, Smolecule.

Always read the supplier’s safety data sheet before working with it.

Spectra

Experimental spectra held by these sources; each link opens the source's own record.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

[1]Hazardous Substances Data Bank (HSDB) · Public domain (US NLM) · via PubChem · retrieved 2026-10-14
[2]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
[3]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
[4]NIST Mass Spectrometry Data Center · Linked only · via PubChem · retrieved 2026-10-14
[5]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
[6]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
·Literature on PubChem

Data last updated 2026-10-14.