Kanamycin (CED0000844)

Record Information
Version1.0
Creation Date2016-05-25 18:25:44 UTC
Update Date2026-05-14 16:58:27 UTC
Accession NumberCHEM022254
Identification
Common NameKanamycin
ClassSmall Molecule
Description
Kanamycin is an organic compound with the chemical formula C18H36N4O11 and an average molecular weight of 484.50 g/mol. Kanamycin belongs to the carbohydrates and carbohydrate conjugates, a subclass of organooxygen compounds within the organic compounds. In terms of its biological activity, the compound is a recorded inhibitor of the small ribosomal subunit protein uS12 (rpsL). The compound is found in or released from five recorded sources, including drinking water and water supply (specifically drinking water) as well as healthcare, pharmaceuticals, and veterinary products, where it is categorized as an antibiotic, antiinfective, aminoglycoside antibacterial, and intestinal antiinfective. Exposure to kanamycin can occur through multiple recorded routes, including oral, intravenous, intraperitoneal, intramuscular, inhalation, respiratory, and irrigation.
Contaminant Type
  • Human Neurotoxin
Chemical Structure
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 Mass484.499 g/mol
Monoisotopic Mass484.238 g/mol
CAS Registry Number8063-07-8
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
SMILESNC[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 IdentifierInChI=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
Biological Properties
StatusDetected and Not Quantified
OriginNot Available
Cellular LocationsNot Available
Biofluid LocationsNot Available
Tissue LocationsNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Organoleptic EffectsNot Available
Physical Properties
StateNot Available
AppearanceNot Available
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot 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
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrumsplash10-02ai-9543500000-ec5e97948b788974569fNot AvailableView Spectrum
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LC-MS/MSLC-MS/MS Spectrumsplash10-00di-2901000023-e1b4c2a4d54a44d851b1Not AvailableView Spectrum
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LC-MS/MSLC-MS/MS Spectrumsplash10-0229-0829000000-f16628522b8cb19f0215Not AvailableView Spectrum
LC-MS/MSLC-MS/MS Spectrumsplash10-03di-0910000000-2474517847292b897b8eNot AvailableView Spectrum
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1D NMR1H NMR Spectrum (1D, D2O, predicted)Not AvailableNot AvailableView Spectrum
1D NMR13C NMR Spectrum (1D, D2O, predicted)Not AvailableNot AvailableView Spectrum
Toxicity Profile
Mechanism of ToxicityNot Available
Carcinogenicity (IARC Classification)Not Available
Minimum Risk LevelNot Available
SymptomsNot Available
TreatmentNot Available
Toxicity Values
Toxicity ValueUnitValue RangeOrganismDose DescriptorRoute of ExposurePredicted or ExperimentalReference
7456.0Log mg/kg[4200:13000]RatLD50oralpredictedNot Available
Health Effects
Health EffectRelationshipDirectionReference
Exposure Sources
Source IDSourceSectorReference
115Drinking waterDrinking water & water supplyNot Available
254Intestinal antiinfectivesHealthcare, pharmaceuticals & veterinary productsNot Available
306AntibioticsHealthcare, pharmaceuticals & veterinary productsNot Available
344Aminoglycoside antibacterialsHealthcare, pharmaceuticals & veterinary productsNot Available
395AntiinfectivesHealthcare, pharmaceuticals & veterinary productsNot Available
Pathways
3 pathways
Targets
StructureProteinUniProt IDOrganismRelationshipDetails
Gap junction beta-2 protein structureClick to view 3D structureGap junction beta-2 proteinP29033HumansPredicted (SEA)0.0778492
Beta-ketoacyl-[acyl-carrier-protein] synthase III structureClick to view 3D structureBeta-ketoacyl-[acyl-carrier-protein] synthase IIIP0A6R0Escherichia coli (strain K12)Predicted (SEA)0.0778492
Click to view 3D structureHuman immunodeficiency virus type 1 REVQ77Y21Human immunodeficiency virus 1Predicted (SEA)0.0778492
Gap junction alpha-1 protein structureClick to view 3D structureGap junction alpha-1 proteinP17302HumansPredicted (SEA)0.389246
Click to view 3D structure3-oxoacyl-[acyl-carrier-protein] synthase 3C3TDZ2Escherichia coliPredicted (SEA)0.0778492
Click to view 3D structureLectinB4EH87Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656/ NCTC 13227 / J2315 / CF5610) (Burkholderia cepacia (strain J2315))Predicted (SEA)1.16774
Click to view 3D structureType 1 fimbrin D-mannose specific adhesinP08191Escherichia coli K-12Predicted (SEA)1.94623
Click to view 3D structureEndo-beta-N-acetylglucosaminidaseQ9ZB22Arthrobacter protophormiaePredicted (SEA)0.778492
CD44 antigen structureClick to view 3D structureCD44 antigenP16070HumansPredicted (SEA)1.08989
Click to view 3D structureCD44 antigenP15379Mus musculusPredicted (SEA)1.08989
Click to view 3D structureN-acetyllactosaminide alpha-1,3-galactosyltransferaseP50127Sus scrofaPredicted (SEA)2.17978
Heparanase structureClick to view 3D structureHeparanaseQ9Y251HumansPredicted (SEA)1.01204
Click to view 3D structureAlpha-amylaseQ7M328Sus scrofa domesticusPredicted (SEA)0.856341
Galectin-3 structureClick to view 3D structureGalectin-3P17931HumansPredicted (SEA)11.1324
Click to view 3D structureKiller cell lectin-like receptor subfamily B member 1AP27471Rattus norvegicusPredicted (SEA)1.40129
Click to view 3D structurePA-I galactophilic lectinQ05097Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG12228)Predicted (SEA)2.72472
Carbonic anhydrase 12 structureClick to view 3D structureCarbonic anhydrase 12O43570HumansPredicted (SEA)802.625
Carbonic anhydrase 7 structureClick to view 3D structureCarbonic anhydrase 7P43166HumansPredicted (SEA)766.737
Carbonic anhydrase 1 structureClick to view 3D structureCarbonic anhydrase 1P00915HumansPredicted (SEA)1236.56
Click to view 3D structureSucrase-isomaltase, intestinalP23739Rattus norvegicusPredicted (SEA)7.39568
Click to view 3D structureLysosomal alpha-glucosidaseQ6P7A9Rattus norvegicusPredicted (SEA)6.15009
Click to view 3D structureCMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1P54751Mus musculusPredicted (SEA)5.29375
Carbonic anhydrase 9 structureClick to view 3D structureCarbonic anhydrase 9Q16790HumansPredicted (SEA)1648.38
Solute carrier family 28 member 3 structureClick to view 3D structureSolute carrier family 28 member 3Q9HAS3HumansPredicted (SEA)33.1638
Click to view 3D structureAdenosine receptor A2aP30543Rattus norvegicusPredicted (SEA)810.644
Concentrations
Not Available
External Links
DrugBank IDDB01172
HMDB IDHMDB0015303
FooDB IDNot Available
Phenol Explorer IDNot Available
KNApSAcK IDC00018690
BiGG IDNot Available
BioCyc IDNot Available
METLIN IDNot Available
PDB IDNot Available
Wikipedia LinkKanamycin
Chemspider ID5810
ChEBI ID17630
PubChem Compound ID6032
Kegg Compound IDC01822
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
1. https://www.ncbi.nlm.nih.gov/pubmed/?term=22907688
2. https://www.ncbi.nlm.nih.gov/pubmed/?term=24336356
3. https://www.ncbi.nlm.nih.gov/pubmed/?term=24566637