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Record Information
Version3.6
Creation Date2012-09-06 15:16:51 UTC
Update Date2016-02-11 01:32:19 UTC
HMDB IDHMDB15303
Secondary Accession NumbersNone
Metabolite Identification
Common NameKanamycin
DescriptionKanamycin is only found in individuals that have used or taken this drug. It is an antibiotic complex produced by Streptomyces kanamyceticus from Japanese soil. Comprises 3 components: kanamycin A, the major component, and kanamycins B and C, the minor components. [PubChem]Aminoglycosides like kanamycin "irreversibly" bind to specific 30S-subunit proteins and 16S rRNA. Specifically Kanamycin binds to four nucleotides of 16S rRNA and a single amino acid of protein S12. This interferes with decoding site in the vicinity of nucleotide 1400 in 16S rRNA of 30S subunit. This region interacts with the wobble base in the anticodon of tRNA. This leads to interference with the initiation complex, misreading of mRNA so incorrect amino acids are inserted into the polypeptide leading to nonfunctional or toxic peptides and the breakup of polysomes into nonfunctional monosomes.
Structure
Thumb
Synonyms
ValueSource
4,6-diamino-2-Hydroxy-1,3-cyclohexane 3,6'diamino-3,6'-dideoxydi-alpha-D-glucosideChEBI
4,6-diamino-2-Hydroxy-1,3-cyclohexylene 3,6'-diamino-3,6'-dideoxydi-D-glucopyranosideChEBI
O-3-amino-3-Deoxy-alpha-D-glucopyranosyl-(1->6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1->4))-2-deoxy-D-streptamineChEBI
4,6-diamino-2-Hydroxy-1,3-cyclohexane 3,6'diamino-3,6'-dideoxydi-a-D-glucosideGenerator
4,6-diamino-2-Hydroxy-1,3-cyclohexane 3,6'diamino-3,6'-dideoxydi-α-D-glucosideGenerator
O-3-amino-3-Deoxy-a-D-glucopyranosyl-(1->6)-O-(6-amino-6-deoxy-a-D-glucopyranosyl-(1->4))-2-deoxy-D-streptamineGenerator
O-3-amino-3-Deoxy-α-D-glucopyranosyl-(1->6)-O-(6-amino-6-deoxy-α-D-glucopyranosyl-(1->4))-2-deoxy-D-streptamineGenerator
AminodeoxykanamycinHMDB
KANHMDB
Kanamycin baseHMDB
Kanamycin sulfateHMDB
Nebramycin factor 5HMDB
Chemical FormulaC18H36N4O11
Average Molecular Weight484.4986
Monoisotopic Molecular Weight484.238058014
IUPAC Name(2R,3S,4S,5R,6R)-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-3-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4,5-triol
Traditional Namekanamycin
CAS Registry Number8063-07-8
SMILES
NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C18H36N4O11/c19-2-6-10(25)12(27)13(28)18(30-6)33-16-5(21)1-4(20)15(14(16)29)32-17-11(26)8(22)9(24)7(3-23)31-17/h4-18,23-29H,1-3,19-22H2/t4-,5+,6-,7-,8+,9-,10-,11-,12+,13-,14-,15+,16-,17-,18-/m1/s1
InChI KeyInChIKey=SBUJHOSQTJFQJX-NOAMYHISSA-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
  • Glucosamine
  • Amino sugar
  • O-glycosyl compound
  • Glycosyl compound
  • Cyclohexylamine
  • Cyclohexanol
  • Oxane
  • Monosaccharide
  • Cyclic alcohol
  • Secondary alcohol
  • Polyol
  • 1,2-diol
  • 1,2-aminoalcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Acetal
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organonitrogen compound
  • Primary aliphatic amine
  • Amine
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Drug
Biofunction
  • Aminoglycosides
  • Anti-Bacterial Agents
  • Protein Synthesis Inhibitors
Application
  • Pharmaceutical
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility9.23e+01 g/LNot Available
LogP-6.3Not Available
Predicted Properties
PropertyValueSource
Water Solubility92.3 mg/mLALOGPS
logP-3.1ALOGPS
logP-7.1ChemAxon
logS-0.72ALOGPS
pKa (Strongest Acidic)12.11ChemAxon
pKa (Strongest Basic)9.75ChemAxon
Physiological Charge4ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area282.61 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity106.13 m3·mol-1ChemAxon
Polarizability47.57 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Kanamycin PathwaySMP00255Not Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01172
  • Not Applicable
details
UrineExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01172
  • Not Applicable
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01172
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID5810
KEGG Compound IDC01822
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkKanamycin
NuGOwiki LinkHMDB15303
Metagene LinkHMDB15303
METLIN IDNot Available
PubChem Compound6032
PDB IDKAN
ChEBI ID17630
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available