Kanamycin C (CED0000853)

Record Information
Version1.0
Creation Date2026-03-31 20:24:08 UTC
Update Date2026-05-20 19:26:08 UTC
SynCED IDCED0000853
Secondary Accession Numbers
  • CHEM057755
Identification
Common NameKanamycin C
ClassSmall Molecule
Description
Kanamycin C is an organic compound with the formula C18H36N4O11 and an average molecular weight of 484.50 g/mol. Kanamycin C belongs to the carbohydrates and carbohydrate conjugates, a subclass of organooxygen compounds within the organic compounds. It is found in or released from one recorded source: healthcare, pharmaceuticals & veterinary products (Antibiotics). Recorded exposure routes for this compound include inhalation and oral administration.
Contaminant TypeNot Available
Chemical Structure
MOLSDFPDBSMILESInChI
SynonymsNot Available
Chemical FormulaC18H36N4O11
Average Molecular Mass484.503 g/mol
Monoisotopic Mass484.238 g/mol
CAS Registry Number2280-32-2
IUPAC Name(2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,5-diol
Traditional Namekanamycin C
SMILESN[C@H]1C[C@@H](N)[C@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](N)[C@H]2O)[C@@H](O)[C@@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1N
InChI IdentifierInChI=1S/C18H36N4O11/c19-4-1-5(20)16(33-18-13(28)8(21)10(25)6(2-23)31-18)14(29)15(4)32-17-9(22)12(27)11(26)7(3-24)30-17/h4-18,23-29H,1-3,19-22H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1
InChI KeyWZDRWYJKESFZMB-FQSMHNGLSA-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
  • 1,2-aminoalcohol
  • Secondary alcohol
  • Organoheterocyclic compound
  • Acetal
  • Oxacycle
  • Alcohol
  • Organonitrogen compound
  • Primary aliphatic amine
  • Hydrocarbon derivative
  • Organopnictogen 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 Solubility89.5 g/LALOGPS
logP-3.1ALOGPS
logP-7.1ChemAxon
logS-0.73ALOGPS
pKa (Strongest Acidic)12.43ChemAxon
pKa (Strongest Basic)9.71ChemAxon
Physiological Charge4ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area282.61 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity106.13 m³·mol⁻¹ChemAxon
Polarizability47.05 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Toxicity Profile
Toxicity Values
Toxicity ValueOrganismDose DescriptorRoute of ExposurePredicted or ExperimentalToxicity RatingReference
8543.0 Log mg/kg [4800:15000]RatLD50oralpredictedNot AvailableNot Available
Toxicity / Toxin ClassNot Available
Mechanism of ToxicityNot Available
Carcinogenicity (IARC Classification)Not Available
Minimum Risk LevelNot Available
SymptomsNot Available
TreatmentNot Available
Health Effects
Health EffectRelationshipDirectionReference
Exposure Sources
Source IDSourceSectorReference
CEDs000306Antibiotics?Antibiotics are synthetic or semi-synthetic compounds used to treat bacterial infections in humans and animals.Healthcare, pharmaceuticals & veterinary productsNot Available
Pathways
0 pathwaysPathway Source: PathBank

No pathways found

No metabolic pathways have been associated with this synthetic chemical

Targets
StructureProteinUniProt IDOrganismRelationshipDetails
Gap junction beta-2 protein structureClick to view 3D structureGap junction beta-2 proteinP29033HumansPredicted (SEA)
Prediction Confidence Score
0.607
Applicability Domain
0.786
Statistical Significance
4.00e-05
Supporting Reference Compounds
2
E-value
0.311397
Beta-ketoacyl-[acyl-carrier-protein] synthase III structureClick to view 3D structureBeta-ketoacyl-[acyl-carrier-protein] synthase IIIP0A6R0Escherichia coli (strain K12)Predicted (SEA)
Prediction Confidence Score
0.58
Applicability Domain
0.9
Statistical Significance
1.00e-05
Supporting Reference Compounds
3
E-value
0.0778492
Click to view 3D structureHuman immunodeficiency virus type 1 REVQ77Y21Human immunodeficiency virus 1Predicted (SEA)
Prediction Confidence Score
0.538
Applicability Domain
0.711
Statistical Significance
1.00e-05
Supporting Reference Compounds
4
E-value
0.0778492
Click to view 3D structure3-oxoacyl-[acyl-carrier-protein] synthase 3C3TDZ2Escherichia coliPredicted (SEA)
Prediction Confidence Score
0.468
Applicability Domain
0.9
Statistical Significance
1.00e-05
Supporting Reference Compounds
2
E-value
0.0778492
Gap junction alpha-1 protein structureClick to view 3D structureGap junction alpha-1 proteinP17302HumansPredicted (SEA)
Prediction Confidence Score
0.415
Applicability Domain
0.415
Statistical Significance
5.00e-05
Supporting Reference Compounds
1
E-value
0.389246
CD44 antigen structureClick to view 3D structureCD44 antigenP16070HumansPredicted (SEA)
Prediction Confidence Score
0.317
Applicability Domain
0.317
Statistical Significance
1.60e-04
Supporting Reference Compounds
1
E-value
1.24559
CD44 antigen structureClick to view 3D structureCD44 antigenP15379Mus musculusPredicted (SEA)
Prediction Confidence Score
0.317
Applicability Domain
0.317
Statistical Significance
1.60e-04
Supporting Reference Compounds
1
E-value
1.24559
Lectin structureClick to view 3D structureLectinB4EH87Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656/ NCTC 13227 / J2315 / CF5610) (Burkholderia cepacia (strain J2315))Predicted (SEA)
Prediction Confidence Score
0.314
Applicability Domain
0.372
Statistical Significance
3.40e-04
Supporting Reference Compounds
3
E-value
2.64687
Type 1 fimbrin D-mannose specific adhesin structureClick to view 3D structureType 1 fimbrin D-mannose specific adhesinP08191Escherichia coli K-12Predicted (SEA)
Prediction Confidence Score
0.31
Applicability Domain
0.372
Statistical Significance
4.60e-04
Supporting Reference Compounds
4
E-value
3.58106
Endo-beta-N-acetylglucosaminidase structureClick to view 3D structureEndo-beta-N-acetylglucosaminidaseQ9ZB22Arthrobacter protophormiaePredicted (SEA)
Prediction Confidence Score
0.29
Applicability Domain
0.29 Low confidence
Statistical Significance
1.30e-04
Supporting Reference Compounds
1
E-value
1.01204
Click to view 3D structureAlpha-amylaseQ7M328Sus scrofa domesticusPredicted (SEA)
Prediction Confidence Score
0.284
Applicability Domain
0.284 Low confidence
Statistical Significance
1.30e-04
Supporting Reference Compounds
1
E-value
1.01204
Click to view 3D structureKiller cell lectin-like receptor subfamily B member 1AP27471Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.282
Applicability Domain
0.323
Statistical Significance
1.00e-04
Supporting Reference Compounds
2
E-value
0.778492
Click to view 3D structureN-acetyllactosaminide alpha-1,3-galactosyltransferaseP50127Sus scrofaPredicted (SEA)
Prediction Confidence Score
0.282
Applicability Domain
0.282 Low confidence
Statistical Significance
4.90e-04
Supporting Reference Compounds
1
E-value
3.81461
Heparanase structureClick to view 3D structureHeparanaseQ9Y251HumansPredicted (SEA)
Prediction Confidence Score
0.28
Applicability Domain
0.711
Statistical Significance
1.40e-04
Supporting Reference Compounds
11
E-value
1.08989
Galectin-3 structureClick to view 3D structureGalectin-3P17931HumansPredicted (SEA)
Prediction Confidence Score
0.273
Applicability Domain
0.37
Statistical Significance
0.0015
Supporting Reference Compounds
23
E-value
11.366
Cytidine deaminase structureClick to view 3D structureCytidine deaminaseP56389Mus musculusPredicted (SEA)
Prediction Confidence Score
0.238
Applicability Domain
0.259 Low confidence
Statistical Significance
0.0029
Supporting Reference Compounds
5
E-value
22.3427
Click to view 3D structureSucrase-isomaltase, intestinalP23739Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.237
Applicability Domain
0.314
Statistical Significance
9.70e-04
Supporting Reference Compounds
25
E-value
7.55137
PA-I galactophilic lectin structureClick to view 3D structurePA-I galactophilic lectinQ05097Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG12228)Predicted (SEA)
Prediction Confidence Score
0.236
Applicability Domain
0.372
Statistical Significance
7.20e-04
Supporting Reference Compounds
4
E-value
5.60514
Carbonic anhydrase 12 structureClick to view 3D structureCarbonic anhydrase 12O43570HumansPredicted (SEA)
Prediction Confidence Score
0.233
Applicability Domain
0.25 Low confidence
Statistical Significance
0.2016
Supporting Reference Compounds
332
E-value
1569.52
Solute carrier family 28 member 3 structureClick to view 3D structureSolute carrier family 28 member 3Q9HAS3HumansPredicted (SEA)
Prediction Confidence Score
0.231
Applicability Domain
0.239 Low confidence
Statistical Significance
0.0045
Supporting Reference Compounds
3
E-value
34.7208
Adenosine deaminase structureClick to view 3D structureAdenosine deaminaseP56658Bos taurusPredicted (SEA)
Prediction Confidence Score
0.23
Applicability Domain
0.258 Low confidence
Statistical Significance
0.006
Supporting Reference Compounds
17
E-value
46.5538
Cytidine deaminase structureClick to view 3D structureCytidine deaminaseP32320HumansPredicted (SEA)
Prediction Confidence Score
0.23
Applicability Domain
0.246 Low confidence
Statistical Significance
0.0027
Supporting Reference Compounds
4
E-value
20.7079
Click to view 3D structureAminoglycoside acetyltransferaseQ70E71Enterococcus duransPredicted (SEA)
Prediction Confidence Score
0.229
Applicability Domain
0.229 Low confidence
Statistical Significance
0.0024
Supporting Reference Compounds
1
E-value
18.4503
Peptidoglycan-N-acetylglucosamine deacetylase structureClick to view 3D structurePeptidoglycan-N-acetylglucosamine deacetylaseQ8DP63Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Predicted (SEA)
Prediction Confidence Score
0.227
Applicability Domain
0.227 Low confidence
Statistical Significance
0.0023
Supporting Reference Compounds
1
E-value
17.5939
Carbonic anhydrase 7 structureClick to view 3D structureCarbonic anhydrase 7P43166HumansPredicted (SEA)
Prediction Confidence Score
0.227
Applicability Domain
0.25 Low confidence
Statistical Significance
0.186
Supporting Reference Compounds
242
E-value
1447.76
Concentrations
Not Available
External Links
DrugBank IDNot Available
HMDB IDNot Available
FooDB IDNot Available
Phenol Explorer IDNot Available
KNApSAcK IDC00018690
BiGG IDNot Available
BioCyc IDCPD-4823
METLIN IDNot Available
PDB IDNot Available
Wikipedia LinkNot Available
Chemspider IDNot Available
ChEBI ID28185
PubChem Compound ID439582
Kegg Compound IDC01823
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General ReferencesNot Available