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Record Information
Version1.0
Created at2020-11-23 18:26:05 UTC
Updated at2021-08-12 19:51:45 UTC
NP-MRD IDNP0002650
Secondary Accession NumbersNone
Natural Product Identification
Common NameKanamycin
Provided ByBMRBBMRB logo
Description Kanamycin is found in Apis cerana, Elateriospermum tapos, Streptomyces hygroscopicus, Streptomyces kanamyceticus, Streptomyces lividans and Streptomyces tendae. It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4,5-triol.
Structure
Thumb
SynonymsNot Available
Chemical FormulaC18H36N4O11
Average Mass484.5030 Da
Monoisotopic Mass484.23806 Da
IUPAC Name(2R,3S,4S,5R,6R)-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4,5-triol
Traditional Name(2R,3S,4S,5R,6R)-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-3-{[(2R,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4,5-triol
CAS Registry NumberNot Available
SMILES
[H]OC([H])([H])[C@]1([H])O[C@@]([H])(O[C@]2([H])[C@@]([H])(O[H])[C@]([H])(O[C@@]3([H])O[C@]([H])(C([H])([H])N([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]3([H])O[H])[C@@]([H])(N([H])[H])C([H])([H])[C@@]2([H])N([H])[H])[C@@]([H])(O[H])[C@]([H])(N([H])[H])[C@@]1([H])O[H]
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-BHEICIAYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Apis ceranaLOTUS Database
Elateriospermum taposLOTUS Database
Streptomyces hygroscopicusLOTUS Database
Streptomyces kanamyceticusLOTUS Database
Streptomyces lividansLOTUS Database
Streptomyces tendaeLOTUS Database
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.1ALOGPS
logP-7.1ChemAxon
logS-0.72ALOGPS
pKa (Strongest Acidic)12.11ChemAxon
pKa (Strongest Basic)9.54ChemAxon
Physiological Charge4ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area282.61 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity106.13 m³·mol⁻¹ChemAxon
Polarizability47.71 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID22886608
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439581
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]