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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:51 UTC
Update Date2022-03-07 02:51:56 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
KantrexHMDB
Kanamycin aHMDB
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
Description Belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are 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
Physiological effectNot Available
Disposition
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility92.3 g/LNot Available
LogP-6.3Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01172 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01172 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01172
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00018690
Chemspider ID5810
KEGG Compound IDC01822
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkKanamycin
METLIN IDNot Available
PubChem Compound6032
PDB IDNot Available
ChEBI ID17630
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1306611
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available