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Record Information
Version2.0
Created at2022-09-09 05:51:11 UTC
Updated at2022-09-09 05:51:11 UTC
NP-MRD IDNP0280196
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-(hydroxymethyl)-6-[(2,3,4-trihydroxy-5-{[4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl)methoxy]oxane-3,4,5-triol
DescriptionValidamycin D belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. 2-(hydroxymethyl)-6-[(2,3,4-trihydroxy-5-{[4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl)methoxy]oxane-3,4,5-triol is found in Streptomyces hygroscopicus. Validamycin D is a very strong basic compound (based on its pKa).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC20H35NO13
Average Mass497.4940 Da
Monoisotopic Mass497.21084 Da
IUPAC Name2-(hydroxymethyl)-6-[(2,3,4-trihydroxy-5-{[4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl)methoxy]oxane-3,4,5-triol
Traditional Name2-(hydroxymethyl)-6-[(2,3,4-trihydroxy-5-{[4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl)methoxy]oxane-3,4,5-triol
CAS Registry NumberNot Available
SMILES
OCC1OC(OCC2CC(NC3C=C(CO)C(O)C(O)C3O)C(O)C(O)C2O)C(O)C(O)C1O
InChI Identifier
InChI=1S/C20H35NO13/c22-3-6-1-8(13(26)16(29)11(6)24)21-9-2-7(12(25)17(30)14(9)27)5-33-20-19(32)18(31)15(28)10(4-23)34-20/h1,7-32H,2-5H2
InChI KeyDZOSEJASWWCMOA-UHFFFAOYSA-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 hygroscopicusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentO-glycosyl compounds
Alternative Parents
Substituents
  • O-glycosyl compound
  • Aminocyclitol or derivatives
  • Aminocyclitol
  • Cyclohexanol
  • Cyclohexylamine
  • Cyclitol or derivatives
  • Monosaccharide
  • Oxane
  • Cyclic alcohol
  • Secondary alcohol
  • 1,2-aminoalcohol
  • Organoheterocyclic compound
  • Polyol
  • Secondary amine
  • Oxacycle
  • Acetal
  • Secondary aliphatic amine
  • Primary alcohol
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Amine
  • Organonitrogen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-2.8ALOGPS
logP-6.9ChemAxon
logS-0.71ALOGPS
pKa (Strongest Acidic)12.08ChemAxon
pKa (Strongest Basic)7.41ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area253.02 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity110.47 m³·mol⁻¹ChemAxon
Polarizability48.87 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound166726
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]