You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version3.6
Creation Date2012-09-06 15:16:49 UTC
Update Date2016-02-11 01:29:15 UTC
HMDB IDHMDB14622
Secondary Accession NumbersNone
Metabolite Identification
Common NameAmikacin
DescriptionAmikacin is a semi-synthetic aminoglycoside antibiotic derived from kanamycin A. Similar to other aminoglycosides, amikacin disrupts bacterial protein synthesis by binding to the 30S ribosome of susceptible organisms. Binding interferes with mRNA binding and tRNA acceptor sites leading to the production of non-functional or toxic peptides. Other mechanisms not fully understood may confer the bactericidal effects of amikacin. Amikacin is also nephrotoxic and ototoxic.
Structure
Thumb
Synonyms
ValueSource
1-N-(L(-)-gamma-amino-alpha-Hydroxybutyryl)kanamycin aChEBI
AmicacinChEBI
Amiglyde-VChEBI
AmikacinaChEBI
AmikacineChEBI
AmikacinumChEBI
AmikavetChEBI
BriclinChEBI
O-3-amino-3-Deoxy-alpha-D-glucopyranosyl-(1->4)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1->6))-N(3)-(4-amino-L-2-hydroxybutyryl)-2-deoxy-L-streptamineChEBI
1-N-(L(-)-g-amino-a-Hydroxybutyryl)kanamycin aGenerator
1-N-(L(-)-γ-amino-α-hydroxybutyryl)kanamycin aGenerator
O-3-amino-3-Deoxy-a-D-glucopyranosyl-(1->4)-O-(6-amino-6-deoxy-a-D-glucopyranosyl-(1->6))-N(3)-(4-amino-L-2-hydroxybutyryl)-2-deoxy-L-streptamineGenerator
O-3-amino-3-Deoxy-α-D-glucopyranosyl-(1->4)-O-(6-amino-6-deoxy-α-D-glucopyranosyl-(1->6))-N(3)-(4-amino-L-2-hydroxybutyryl)-2-deoxy-L-streptamineGenerator
Amikacin baseHMDB
Amikacin dihydrateHMDB
Amikacin sulfateHMDB
ANTIBIOTIC BB-K8HMDB
BB-K8HMDB
Chemical FormulaC22H43N5O13
Average Molecular Weight585.6025
Monoisotopic Molecular Weight585.285736487
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
Traditional Nameamikacin
CAS Registry Number37517-28-5
SMILES
NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](N)[C@H]1O
InChI Identifier
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 KeyInChIKey=LKCWBDHBTVXHDL-RMDFUYIESA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as amino sugars. These are sugars having one alcoholic hydroxy group replaced by an amino group; systematically known as x-amino-x-deoxymonosaccharides. These compounds do not include Glycosylamines.
KingdomOrganic compounds
Super ClassOrganooxygen compounds
ClassCarbohydrates and carbohydrate conjugates
Sub ClassAminosaccharides
Direct ParentAmino sugars
Alternative Parents
Substituents
  • 4,6-disubstituted 2-deoxystreptamine
  • Aminoglycoside core
  • 2-deoxystreptamine aminoglycoside
  • Gamma amino acid or derivatives
  • Glucosamine
  • Amino sugar
  • O-glycosyl compound
  • Glycosyl compound
  • Cyclohexylamine
  • Cyclohexanol
  • Fatty acyl
  • Oxane
  • N-acyl-amine
  • Monosaccharide
  • Fatty amide
  • Cyclic alcohol
  • 1,3-aminoalcohol
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Polyol
  • Carboxamide group
  • 1,2-diol
  • 1,2-aminoalcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Carboxylic acid amide
  • Acetal
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Drug
Biofunction
  • Aminoglycosides
  • Anti-Bacterial Agents
Application
  • Pharmaceutical
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point203 - 204 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility4.97e+01 g/LNot Available
LogP-7.4Not Available
Predicted Properties
PropertyValueSource
Water Solubility49.7 mg/mLALOGPS
logP-3.2ALOGPS
logP-8.6ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)12.1ChemAxon
pKa (Strongest Basic)9.79ChemAxon
Physiological Charge4ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area331.94 Å2ChemAxon
Rotatable Bond Count10ChemAxon
Refractivity129.84 m3·mol-1ChemAxon
Polarizability58.2 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Amikacin PathwaySMP00253Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00479
  • Not Applicable
details
UrineExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00479
  • Not Applicable
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00479
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID34635
KEGG Compound IDC06820
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAmikacin
NuGOwiki LinkHMDB14622
Metagene LinkHMDB14622
METLIN IDNot Available
PubChem Compound37768
PDB IDNot Available
ChEBI ID2637
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Edson RS, Terrell CL: The aminoglycosides. Mayo Clin Proc. 1999 May;74(5):519-28. [10319086 ]