Kanamycin B (CED0011570)

Record Information

Version

1.0

Creation Date

2016-05-22 03:42:15 UTC

Update Date

2026-05-14 19:35:54 UTC

SynCED ID

CED0011570

Secondary Accession Numbers

CHEM016746

Identification

Common Name

Kanamycin B

Class

Small Molecule

Description

Kanamycin B is an organic compound with the formula C18H37N5O10 and an average molecular weight of 483.51 g/mol. Kanamycin B 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 Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2'-Amino-2'-deoxykanamycin	ChEBI
Nebramycin factor 5	ChEBI
Nebramycin V	ChEBI
O-3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1->4)-O-(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl-(1->6))-2-deoxy-D-streptamine	ChEBI
Kanamycin b	Kegg
O-3-Amino-3-deoxy-a-D-glucopyranosyl-(1->4)-O-(2,6-diamino-2,6-dideoxy-a-D-glucopyranosyl-(1->6))-2-deoxy-D-streptamine	Generator
O-3-Amino-3-deoxy-α-D-glucopyranosyl-(1->4)-O-(2,6-diamino-2,6-dideoxy-α-D-glucopyranosyl-(1->6))-2-deoxy-D-streptamine	Generator
Bekanamycin	ChEBI
Kanendomycin	MeSH
Bekanamycin sulfate (1:1)	MeSH
Aminodeoxykanamycin	MeSH
Bekanamycin sulfate	MeSH

Chemical Formula

C₁₈H₃₇N₅O₁₀

Average Molecular Mass

483.514 g/mol

Monoisotopic Mass

483.254 g/mol

CAS Registry Number

4696-76-8

IUPAC Name

(2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,5-diol

Traditional Name

(2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,5-diol

SMILES

[H][C@]1(N)C[C@@]([H])(N)[C@]([H])(O[C@@]2([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(N)[C@@]2([H])O)[C@@]([H])(O)[C@]1([H])O[C@@]1([H])O[C@]([H])(CN)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])N

InChI Identifier

InChI=1S/C18H37N5O10/c19-2-6-11(26)12(27)9(23)17(30-6)32-15-4(20)1-5(21)16(14(15)29)33-18-13(28)8(22)10(25)7(3-24)31-18/h4-18,24-29H,1-3,19-23H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13+,14-,15+,16-,17+,18+/m0/s1

InChI Key

SKKLOUVUUNMCJE-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

4,6-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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

kanamycins (CHEBI:28098 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Organoleptic Effects

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	75.9 g/L	ALOGPS
logP	-3	ALOGPS
logP	-7.2	ChemAxon
logS	-0.8	ALOGPS
pKa (Strongest Acidic)	12.49	ChemAxon
pKa (Strongest Basic)	9.76	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	288.4 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	107.79 m³·mol⁻¹	ChemAxon
Polarizability	47.72 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0aw9-0219800000-8bffd56b3f946b4cdee9	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-08fr-0917100000-f152e80b7cd2e86983e6	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-08fv-5914000000-9311fd0d8e2f4f2007c8	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-001r-9366600000-242a7eebeb0e0273b309	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-006x-9536300000-520e4218f16dc8c4b90d	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0udi-5793000000-2ae8be694bf4f51aa2b2	Not Available	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, H₂O, predicted)	Not Available	Not Available	View Spectrum
1D NMR	¹H NMR Spectrum (1D, H₂O, predicted)	Not Available	Not Available	View Spectrum

Toxicity Profile

Toxicity Values

Toxicity Value	Organism	Dose Descriptor	Route of Exposure	Predicted or Experimental	Toxicity Rating	Reference
7602.0 Log mg/kg [4300:14000]	Rat	LD50	oral	predicted	Not Available	Not Available

Toxicity / Toxin Class

Not Available

Mechanism of Toxicity

Not Available

Carcinogenicity (IARC Classification)

Not Available

Minimum Risk Level

Not Available

Symptoms

Not Available

Treatment

Not Available

Health Effects

Health Effect	Relationship	Direction	Description	Reference

Exposure Sources

Source ID	Source	Sector	Reference
CEDs000306	Antibiotics?Antibiotics are synthetic or semi-synthetic compounds used to treat bacterial infections in humans and animals.	Healthcare, pharmaceuticals & veterinary products	Not Available
CEDs000511	Conductors Or Conductive Bodies Characterised By The Conductive Materials?Conductors, or conductive bodies, are materials that allow the flow of electrical current, typically made from metals such as copper, aluminum, or silver.	Electrical & Electronic Equipment	PubChem
CEDs000518	Electrically Stimulated Smoking Devices?Electrically stimulated smoking devices, commonly known as e-cigarettes or vape pens, utilize electrical components to heat a liquid solution, often containing nicotine, flavorings, and other additives, to produce an aerosol for inhalation.	Electrical & Electronic Equipment	PubChem
CEDs000545	Food Preservation?Food preservation often involves the use of synthetic chemicals, such as preservatives, flavor enhancers, and color additives, to extend shelf life and enhance the sensory qualities of food products.	Food, food processing & cookware	PubChem
CEDs000569	Tobacco Smoke Filters?Tobacco smoke filters are designed to reduce the inhalation of harmful substances in cigarette smoke, including tar and other particulate matter.	Household cleaning & consumer products	PubChem
CEDs000580	Manufacture Preparation Of Tobacco Products?The manufacture and preparation of tobacco products involve various processes that can result in the introduction of synthetic chemicals into the environment.	Industrial manufacturing & chemical processing	PubChem
CEDs000581	Paper Making Machines?Paper making machines utilize various synthetic chemicals throughout the production process, including additives, coatings, and bleaching agents.	Industrial manufacturing & chemical processing	PubChem
CEDs000632	Apparel?Apparel production often involves the use of various synthetic chemicals, including dyes, finishing agents, and preservatives.	Textiles, leather & furnishings	PubChem
CEDs000696	Nanotechnology?Nanotechnology involves the manipulation of materials at the molecular or atomic level, typically within the range of 1 to 100 nanometers.	Industrial manufacturing & chemical processing	PubChem
CEDs000740	Paper?Paper production involves the processing of wood fibers and the use of various chemicals, which can lead to synthetic chemical contamination.	Paper, pulp & fiber products	PubChem
CEDs000744	Water, Wastewater, & Sewage Treatment?Water, wastewater, and sewage treatment processes are critical for managing and mitigating pollutants in water systems.	Wastewater, sanitation & biosolids	PubChem

Pathways

0 pathwaysPathway Source: PathBank

No pathways found

No metabolic pathways have been associated with this synthetic chemical

Targets

Structure	Protein	UniProt ID	Organism	Relationship	Details
Click to view 3D structure	Gap junction beta-2 protein	P29033	Humans	Predicted (SEA)	Prediction Confidence Score 0.687 Applicability Domain 0.881 Statistical Significance 1.00e-05 Supporting Reference Compounds 2 E-value 0.0778492
Click to view 3D structure	Beta-ketoacyl-[acyl-carrier-protein] synthase III	P0A6R0	Escherichia coli (strain K12)	Predicted (SEA)	Prediction Confidence Score 0.644 Applicability Domain 1.0 Statistical Significance 1.00e-05 Supporting Reference Compounds 3 E-value 0.0778492
Click to view 3D structure	Human immunodeficiency virus type 1 REV	Q77Y21	Human immunodeficiency virus 1	Predicted (SEA)	Prediction Confidence Score 0.583 Applicability Domain 0.761 Statistical Significance 1.00e-05 Supporting Reference Compounds 4 E-value 0.0778492
Click to view 3D structure	3-oxoacyl-[acyl-carrier-protein] synthase 3	C3TDZ2	Escherichia coli	Predicted (SEA)	Prediction Confidence Score 0.517 Applicability Domain 1.0 Statistical Significance 1.00e-05 Supporting Reference Compounds 2 E-value 0.0778492
Click to view 3D structure	Gap junction alpha-1 protein	P17302	Humans	Predicted (SEA)	Prediction Confidence Score 0.477 Applicability Domain 0.477 Statistical Significance 5.00e-05 Supporting Reference Compounds 1 E-value 0.389246
Click to view 3D structure	CD44 antigen	P16070	Humans	Predicted (SEA)	Prediction Confidence Score 0.299 Applicability Domain 0.299 Low confidence Statistical Significance 2.00e-04 Supporting Reference Compounds 1 E-value 1.55698
Click to view 3D structure	CD44 antigen	P15379	Mus musculus	Predicted (SEA)	Prediction Confidence Score 0.299 Applicability Domain 0.299 Low confidence Statistical Significance 2.00e-04 Supporting Reference Compounds 1 E-value 1.55698
Click to view 3D structure	Endo-beta-N-acetylglucosaminidase	Q9ZB22	Arthrobacter protophormiae	Predicted (SEA)	Prediction Confidence Score 0.292 Applicability Domain 0.292 Low confidence Statistical Significance 1.30e-04 Supporting Reference Compounds 1 E-value 1.01204
Click to view 3D structure	Lectin	B4EH87	Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656/ NCTC 13227 / J2315 / CF5610) (Burkholderia cepacia (strain J2315))	Predicted (SEA)	Prediction Confidence Score 0.289 Applicability Domain 0.34 Statistical Significance 5.50e-04 Supporting Reference Compounds 3 E-value 4.28171
Click to view 3D structure	Type 1 fimbrin D-mannose specific adhesin	P08191	Escherichia coli K-12	Predicted (SEA)	Prediction Confidence Score 0.286 Applicability Domain 0.34 Statistical Significance 7.10e-04 Supporting Reference Compounds 4 E-value 5.52729
Click to view 3D structure	Heparanase	Q9Y251	Humans	Predicted (SEA)	Prediction Confidence Score 0.284 Applicability Domain 0.761 Statistical Significance 1.40e-04 Supporting Reference Compounds 11 E-value 1.08989
Click to view 3D structure	Alpha-amylase	Q7M328	Sus scrofa domesticus	Predicted (SEA)	Prediction Confidence Score 0.268 Applicability Domain 0.268 Low confidence Statistical Significance 1.50e-04 Supporting Reference Compounds 1 E-value 1.16774
Click to view 3D structure	N-acetyllactosaminide alpha-1,3-galactosyltransferase	P50127	Sus scrofa	Predicted (SEA)	Prediction Confidence Score 0.267 Applicability Domain 0.267 Low confidence Statistical Significance 6.80e-04 Supporting Reference Compounds 1 E-value 5.29375
Click to view 3D structure	Killer cell lectin-like receptor subfamily B member 1A	P27471	Rattus norvegicus	Predicted (SEA)	Prediction Confidence Score 0.265 Applicability Domain 0.303 Statistical Significance 2.00e-04 Supporting Reference Compounds 2 E-value 1.55698
Click to view 3D structure	Galectin-3	P17931	Humans	Predicted (SEA)	Prediction Confidence Score 0.258 Applicability Domain 0.345 Statistical Significance 0.0017 Supporting Reference Compounds 23 E-value 13.5458
Click to view 3D structure	Aminoglycoside acetyltransferase	Q70E71	Enterococcus durans	Predicted (SEA)	Prediction Confidence Score 0.231 Applicability Domain 0.231 Low confidence Statistical Significance 0.0022 Supporting Reference Compounds 1 E-value 17.5161
Click to view 3D structure	Cytidine deaminase	P56389	Mus musculus	Predicted (SEA)	Prediction Confidence Score 0.222 Applicability Domain 0.241 Low confidence Statistical Significance 0.0039 Supporting Reference Compounds 5 E-value 30.2833
Click to view 3D structure	Sucrase-isomaltase, intestinal	P23739	Rattus norvegicus	Predicted (SEA)	Prediction Confidence Score 0.221 Applicability Domain 0.291 Low confidence Statistical Significance 0.0012 Supporting Reference Compounds 25 E-value 9.49761
Click to view 3D structure	Carbonic anhydrase 12	O43570	Humans	Predicted (SEA)	Prediction Confidence Score 0.219 Applicability Domain 0.235 Low confidence Statistical Significance 0.2971 Supporting Reference Compounds 332 E-value 2313.13
Click to view 3D structure	Transient receptor potential cation channel subfamily V member 1	Q8NER1	Humans	Predicted (SEA)	Prediction Confidence Score 0.219 Applicability Domain 0.723 Statistical Significance 0.1918 Supporting Reference Compounds 104 E-value 1493.3
Click to view 3D structure	PA-I galactophilic lectin	Q05097	Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG12228)	Predicted (SEA)	Prediction Confidence Score 0.219 Applicability Domain 0.34 Statistical Significance 9.60e-04 Supporting Reference Compounds 4 E-value 7.47353
Click to view 3D structure	Ribonuclease pancreatic	P61823	Bos taurus	Predicted (SEA)	Prediction Confidence Score 0.217 Applicability Domain 0.217 Low confidence Statistical Significance 0.0032 Supporting Reference Compounds 1 E-value 24.6782
Click to view 3D structure	Solute carrier family 28 member 3	Q9HAS3	Humans	Predicted (SEA)	Prediction Confidence Score 0.217 Applicability Domain 0.225 Low confidence Statistical Significance 0.0054 Supporting Reference Compounds 3 E-value 42.2721
Click to view 3D structure	Adenosine deaminase	P56658	Bos taurus	Predicted (SEA)	Prediction Confidence Score 0.216 Applicability Domain 0.242 Low confidence Statistical Significance 0.0079 Supporting Reference Compounds 17 E-value 61.8123
Click to view 3D structure	Cytidine deaminase	P32320	Humans	Predicted (SEA)	Prediction Confidence Score 0.215 Applicability Domain 0.23 Low confidence Statistical Significance 0.0038 Supporting Reference Compounds 4 E-value 29.5049