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Record Information
Version2.0
Created at2020-12-09 00:49:33 UTC
Updated at2021-07-15 16:46:56 UTC
NP-MRD IDNP0003630
Secondary Accession NumbersNone
Natural Product Identification
Common NameDestomycin C
Provided ByNPAtlasNPAtlas Logo
Description(2S,3'R,3aR,4S,4'S,5'R,6S,6'R,7S,7aR)-6'-[(1R)-1-amino-2-hydroxyethyl]-4-{[(2R,3S,5S,6R)-2,6-dihydroxy-3,5-bis(methylamino)cyclohexyl]oxy}-6-(hydroxymethyl)-tetrahydro-3aH-spiro[[1,3]dioxolo[4,5-c]pyran-2,2'-oxane]-3',4',5',7-tetrol belongs to the class of organic compounds known as 2-deoxystreptamine aminoglycosides. These are aminoglycosides containing the 2-deoxystreptamine (1,3-diaminocyclohexane-4,5,6-triol) core. Destomycin C is found in Streptomyces rimofaciens and Streptomyces rimofaciens n. sp.. Destomycin C was first documented in 1975 (PMID: 1126870). Based on a literature review very few articles have been published on (2S,3'R,3aR,4S,4'S,5'R,6S,6'R,7S,7aR)-6'-[(1R)-1-amino-2-hydroxyethyl]-4-{[(2R,3S,5S,6R)-2,6-dihydroxy-3,5-bis(methylamino)cyclohexyl]oxy}-6-(hydroxymethyl)-tetrahydro-3aH-spiro[[1,3]dioxolo[4,5-c]pyran-2,2'-oxane]-3',4',5',7-tetrol.
Structure
Thumb
SynonymsNot Available
Chemical FormulaC21H39N3O13
Average Mass541.5510 Da
Monoisotopic Mass541.24829 Da
IUPAC Name(2S,3'R,3aR,4S,4'S,5'R,6S,6'R,7S,7aR)-6'-[(1R)-1-amino-2-hydroxyethyl]-4-{[(2R,3S,5S,6R)-2,6-dihydroxy-3,5-bis(methylamino)cyclohexyl]oxy}-6-(hydroxymethyl)-tetrahydro-3aH-spiro[[1,3]dioxolo[4,5-c]pyran-2,2'-oxane]-3',4',5',7-tetrol
Traditional Name(2S,3'R,3aR,4S,4'S,5'R,6S,6'R,7S,7aR)-6'-[(1R)-1-amino-2-hydroxyethyl]-4-{[(2R,3S,5S,6R)-2,6-dihydroxy-3,5-bis(methylamino)cyclohexyl]oxy}-6-(hydroxymethyl)-tetrahydro-3aH-spiro[[1,3]dioxolo[4,5-c]pyran-2,2'-oxane]-3',4',5',7-tetrol
CAS Registry NumberNot Available
SMILES
CN[C@H]1C[C@H](NC)[C@@H](O)C(O[C@@H]2O[C@@H](CO)[C@H](O)[C@H]3O[C@@]4(O[C@@H]23)O[C@H]([C@H](N)CO)[C@H](O)[C@H](O)[C@H]4O)[C@@H]1O
InChI Identifier
InChI=1S/C21H39N3O13/c1-23-7-3-8(24-2)11(28)16(10(7)27)34-20-18-17(12(29)9(5-26)33-20)36-21(37-18)19(32)14(31)13(30)15(35-21)6(22)4-25/h6-20,23-32H,3-5,22H2,1-2H3/t6-,7+,8+,9+,10-,11-,12+,13-,14+,15-,17-,18-,19-,20+,21+/m1/s1
InChI KeyXQRJFJIKNNEPNI-UNGVYMPWSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces rimofaciensNPAtlas
Streptomyces rimofaciens n. sp.Bacteria
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 2-deoxystreptamine aminoglycosides. These are aminoglycosides containing the 2-deoxystreptamine (1,3-diaminocyclohexane-4,5,6-triol) core.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct Parent2-deoxystreptamine aminoglycosides
Alternative Parents
Substituents
  • 2-deoxystreptamine aminoglycoside
  • O-glycosyl compound
  • Glycosyl compound
  • Disaccharide
  • Dioxolopyran
  • Aminocyclitol or derivatives
  • Ortho ester
  • Cyclohexylamine
  • Cyclohexanol
  • Carboxylic acid orthoester
  • Oxane
  • Cyclitol or derivatives
  • Cyclic alcohol
  • Meta-dioxolane
  • Secondary alcohol
  • Orthocarboxylic acid derivative
  • 1,2-aminoalcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Polyol
  • Secondary aliphatic amine
  • Acetal
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organonitrogen compound
  • Primary aliphatic amine
  • Amine
  • Alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
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-2.4ALOGPS
logP-5.9ChemAxon
logS-0.54ALOGPS
pKa (Strongest Acidic)11.41ChemAxon
pKa (Strongest Basic)9.6ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area258.07 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity118.83 m³·mol⁻¹ChemAxon
Polarizability53.35 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA021164
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78443161
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139589185
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Shimura M, Sekizawa Y, Iinuma K, Naganawa H, Kondo S: Destomycin C, a new member of destomycin family antibiotics. J Antibiot (Tokyo). 1975 Jan;28(1):83-4. doi: 10.7164/antibiotics.28.83. [PubMed:1126870 ]