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Record Information
Version4.0
Creation Date2012-09-06 15:16:51 UTC
Update Date2017-09-27 08:27:53 UTC
HMDB IDHMDB0015303
Secondary Accession Numbers
  • HMDB15303
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
KantrexMeSH
Kanamycin aMeSH
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 KeySBUJHOSQTJFQJX-NOAMYHISSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct Parent4,6-disubstituted 2-deoxystreptamines
Alternative Parents
Substituents
  • 4,6-disubstituted 2-deoxystreptamine
  • Glycosyl compound
  • O-glycosyl compound
  • Aminocyclitol or derivatives
  • Cyclohexanol
  • Cyclohexylamine
  • Cyclitol or derivatives
  • Monosaccharide
  • Oxane
  • Cyclic alcohol
  • Secondary alcohol
  • 1,2-aminoalcohol
  • Polyol
  • Organoheterocyclic compound
  • Acetal
  • Oxacycle
  • Alcohol
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organonitrogen compound
  • Organic nitrogen compound
  • Amine
  • Primary alcohol
  • Primary amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Role

Industrial application:

  Pharmaceutical industry:

    Antimicrobial agent:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility92.3 g/LNot Available
LogP-6.3Not Available
Predicted Properties
PropertyValueSource
Water Solubility92.3 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity106.13 m³·mol⁻¹ChemAxon
Polarizability47.57 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-02ai-9543500000-ec5e97948b788974569fView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-03e9-9221213000-0d2218e341a1e472caabView in MoNA
LC-MS/MSLC-MS/MS Spectrum - DI-ESI-Ion Trap , Positivesplash10-00di-2901000023-e1b4c2a4d54a44d851b1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - DI-ESI-Hybrid FT , Positivesplash10-00di-2901000023-e1b4c2a4d54a44d851b1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0cki-0409400000-07db8e9644e08a0b579cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-08fr-0916000000-7a0e33b6f175ffea2627View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-2902000000-8b1a93b98307c301f6a5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0089-4977800000-03d3651e5cdc96e9168bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fdo-6649300000-8fcfeb60017d81263bcbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0r6r-4921000000-9827643510b1b217ad83View in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
Kanamycin PathwayPw000353Pw000353 greyscalePw000353 simpleNot Available
Displaying 1 entry
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB01172 details
UrineExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB01172 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
METLIN IDNot Available
PubChem Compound6032
PDB IDKAN
ChEBI ID17630
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available