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Record Information
Version2.0
Created at2022-09-10 01:21:58 UTC
Updated at2022-09-10 01:21:59 UTC
NP-MRD IDNP0293388
Secondary Accession NumbersNone
Natural Product Identification
Common Name(3s)-n-[(2r,3r,4s,5r,6r)-2-{[(3as,7r,7as)-4,7-dihydroxy-3h,3ah,6h,7h,7ah-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-(c-hydroxycarbonimidoyloxy)-6-(hydroxymethyl)oxan-3-yl]-3,6-diaminohexanimidic acid
DescriptionStreptothricin F, also known as racemomycin a or yazumycin a, belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). (3s)-n-[(2r,3r,4s,5r,6r)-2-{[(3as,7r,7as)-4,7-dihydroxy-3h,3ah,6h,7h,7ah-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-(c-hydroxycarbonimidoyloxy)-6-(hydroxymethyl)oxan-3-yl]-3,6-diaminohexanimidic acid is found in Streptomyces griseochromogenes, Streptomyces griseus, Streptomyces lavendulae, Streptomyces nojiriensis, Streptomyces qinlingensis and Streptomyces roseolilacinus. (3s)-n-[(2r,3r,4s,5r,6r)-2-{[(3as,7r,7as)-4,7-dihydroxy-3h,3ah,6h,7h,7ah-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-(c-hydroxycarbonimidoyloxy)-6-(hydroxymethyl)oxan-3-yl]-3,6-diaminohexanimidic acid was first documented in 2006 (PMID: 16641084). Based on a literature review very few articles have been published on streptothricin F (PMID: 19897889).
Structure
Thumb
Synonyms
ValueSource
Antibiotic S 15-1aChEBI
Racemomycin aChEBI
StreptothricinChEBI
Streptothricin VIChEBI
Yazumycin aChEBI
S15-1-aMeSH
Chemical FormulaC19H34N8O8
Average Mass502.5290 Da
Monoisotopic Mass502.24996 Da
IUPAC Name(3S)-N-[(2R,3R,4S,5R,6R)-2-{[(3aS,7R,7aS)-4,7-dihydroxy-3H,3aH,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-(C-hydroxycarbonimidoyloxy)-6-(hydroxymethyl)oxan-3-yl]-3,6-diaminohexanimidic acid
Traditional Name(3S)-N-[(2R,3R,4S,5R,6R)-2-{[(3aS,7R,7aS)-4,7-dihydroxy-3H,3aH,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-4-hydroxy-5-(C-hydroxycarbonimidoyloxy)-6-(hydroxymethyl)oxan-3-yl]-3,6-diaminohexanimidic acid
CAS Registry NumberNot Available
SMILES
NCCC[C@H](N)CC(O)=N[C@H]1[C@H](NC2=N[C@H]3[C@H](N2)C(O)=NC[C@H]3O)O[C@H](CO)[C@H](OC(O)=N)[C@H]1O
InChI Identifier
InChI=1S/C19H34N8O8/c20-3-1-2-7(21)4-10(30)24-13-14(31)15(35-18(22)33)9(6-28)34-17(13)27-19-25-11-8(29)5-23-16(32)12(11)26-19/h7-9,11-15,17,28-29,31H,1-6,20-21H2,(H2,22,33)(H,23,32)(H,24,30)(H2,25,26,27)/t7-,8+,9+,11+,12-,13+,14-,15-,17+/m0/s1
InChI KeyNRAUADCLPJTGSF-VLSXYIQESA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces griseochromogenesLOTUS Database
Streptomyces griseusLOTUS Database
Streptomyces lavendulaeLOTUS Database
Streptomyces nojiriensisLOTUS Database
Streptomyces qinlingensisLOTUS Database
Streptomyces roseolilacinusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • Hexose monosaccharide
  • Beta amino acid or derivatives
  • N-glycosyl compound
  • Alpha-amino acid or derivatives
  • Imidazopyridine
  • Delta-lactam
  • Piperidinone
  • Fatty amide
  • Fatty acyl
  • Monosaccharide
  • N-acyl-amine
  • Oxane
  • Piperidine
  • 2-imidazoline
  • Carbamic acid ester
  • Amino acid or derivatives
  • Carboxamide group
  • Guanidine
  • Lactam
  • Carbonic acid derivative
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Carboxylic acid derivative
  • Organic 1,3-dipolar compound
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Primary alcohol
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Amine
  • Primary aliphatic amine
  • Alcohol
  • Organonitrogen compound
  • Organopnictogen compound
  • Carbonyl group
  • Primary amine
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
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-10ChemAxon
pKa (Strongest Acidic)-3.4ChemAxon
pKa (Strongest Basic)11.29ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area276.87 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity128.16 m³·mol⁻¹ChemAxon
Polarizability48.91 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 ID170645
KEGG Compound IDC19785
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound197034
PDB IDNot Available
ChEBI ID60821
Good Scents IDNot Available
References
General References
  1. Hamano Y, Matsuura N, Kitamura M, Takagi H: A novel enzyme conferring streptothricin resistance alters the toxicity of streptothricin D from broad-spectrum to bacteria-specific. J Biol Chem. 2006 Jun 23;281(25):16842-16848. doi: 10.1074/jbc.M602294200. Epub 2006 Apr 26. [PubMed:16641084 ]
  2. Maruyama C, Hamano Y: The biological function of the bacterial isochorismatase-like hydrolase SttH. Biosci Biotechnol Biochem. 2009 Nov;73(11):2494-500. doi: 10.1271/bbb.90499. Epub 2009 Nov 7. [PubMed:19897889 ]
  3. LOTUS database [Link]