5,6-Dihydrouridine (CHEM021782)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-05-25 18:12:23 UTC
Update Date2016-11-09 01:17:22 UTC
Accession NumberCHEM021782
Identification
Common Name5,6-Dihydrouridine
ClassSmall Molecule
DescriptionThe uridine derivative obtained by formal hydrogenation of the endocyclic double bond in the uracil ring.
Contaminant Sources
  • FooDB Chemicals
  • HMDB Contaminants - Urine
Contaminant TypeNot Available
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
1-beta-D-RibofuranosylhydrouracilChEBI
3,4-DihydrouridineChEBI
DChEBI
1-b-D-RibofuranosylhydrouracilGenerator
1-Β-D-ribofuranosylhydrouracilGenerator
Dihydro-1-b-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
Dihydro-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
DihydrouridineHMDB
5,6-DihydrouridineMeSH
Chemical FormulaC9H14N2O6
Average Molecular Mass246.217 g/mol
Monoisotopic Mass246.085 g/mol
CAS Registry Number5627-05-4
IUPAC Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,3-diazinane-2,4-dione
Traditional Namedihydrouridine
SMILESOC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O
InChI IdentifierInChI=1S/C9H14N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h4,6-8,12,14-15H,1-3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1
InChI KeyZPTBLXKRQACLCR-XVFCMESISA-N
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
  • N-glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Hydropyrimidine
  • 1,2,5,6-tetrahydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Tetrahydrofuran
  • Secondary alcohol
  • Carbonic acid derivative
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organopnictogen compound
  • Carbonyl group
  • Alcohol
  • Primary alcohol
  • Organic nitrogen compound
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginNot Available
Cellular LocationsNot Available
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateNot Available
AppearanceNot Available
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
Predicted Properties
PropertyValueSource
Water Solubility231 g/LALOGPS
logP-2.1ALOGPS
logP-2.8ChemAxon
logS-0.03ALOGPS
pKa (Strongest Acidic)11.59ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area119.33 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity52.34 m³·mol⁻¹ChemAxon
Polarizability22.98 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-9630000000-15e433fd50f5283e7c70Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0fa2-5977600000-2e6dc8e47acc572f91e7Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, PositiveNot AvailableSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-1920000000-6709bfe12a99399905aeSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-8900000000-8c868a51dd1b65e8911fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014m-9500000000-65ec5beb0c86d7c307b3Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01ot-2690000000-33fe0d39759c16898235Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9100000000-bb26ee994aafc4e96a2eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-4c20e49ada219697c154Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0920000000-4ef817592c10e76e901dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-2920000000-e1ff0efd002a4870b8d2Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01b9-9700000000-c671b5ded8fa9d4e6734Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01r2-0590000000-4d20d79523dcba08b44aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0hfw-4940000000-4e7d076c3dc715e35ccfSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-d9747b2acc3e65b6ad8cSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityNot Available
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)Not Available
Uses/SourcesNot Available
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Concentrations
Not Available
DrugBank IDNot Available
HMDB IDHMDB0000497
FooDB IDFDB022076
Phenol Explorer IDNot Available
KNApSAcK IDNot Available
BiGG IDNot Available
BioCyc IDNot Available
METLIN ID5483
PDB IDNot Available
Wikipedia LinkDihydrouridine
Chemspider ID85115
ChEBI ID23774
PubChem Compound ID94312
Kegg Compound IDNot Available
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
1. https://www.ncbi.nlm.nih.gov/pubmed/?term=12003496
2. https://www.ncbi.nlm.nih.gov/pubmed/?term=19139092
3. https://www.ncbi.nlm.nih.gov/pubmed/?term=19488969
4. https://www.ncbi.nlm.nih.gov/pubmed/?term=21628433
5. https://www.ncbi.nlm.nih.gov/pubmed/?term=22123979
6. https://www.ncbi.nlm.nih.gov/pubmed/?term=2283377
7. https://www.ncbi.nlm.nih.gov/pubmed/?term=2692708
8. https://www.ncbi.nlm.nih.gov/pubmed/?term=2817393
9. https://www.ncbi.nlm.nih.gov/pubmed/?term=3512560
10. https://www.ncbi.nlm.nih.gov/pubmed/?term=4910242
11. https://www.ncbi.nlm.nih.gov/pubmed/?term=5133096
12. https://www.ncbi.nlm.nih.gov/pubmed/?term=5139934
13. https://www.ncbi.nlm.nih.gov/pubmed/?term=5572899
14. https://www.ncbi.nlm.nih.gov/pubmed/?term=5640373
15. https://www.ncbi.nlm.nih.gov/pubmed/?term=8299222
16. https://www.ncbi.nlm.nih.gov/pubmed/?term=8555190
17. https://www.ncbi.nlm.nih.gov/pubmed/?term=8604341
18. https://www.ncbi.nlm.nih.gov/pubmed/?term=8774907
19. https://www.ncbi.nlm.nih.gov/pubmed/?term=9417777
20. Cerutti, Peter; Kondo, Yoshikazu; Landis, W. R.; Witkop, Bernhard. Photoreduction of uridine and reduction of dihydrouridine with sodium borohydride. Journal of the American Chemical Society (1968), 90(3), 771-5.
21. Reimer ML, Schram KH, Nakano K, Yasaka T: The identification of 5,6-dihydrouridine in normal human urine by combined gas chromatography/mass spectrometry. Anal Biochem. 1989 Sep;181(2):302-8.
22. Topp H, Duden R, Schoch G: 5,6-Dihydrouridine: a marker ribonucleoside for determining whole body degradation rates of transfer RNA in man and rats. Clin Chim Acta. 1993 Sep 17;218(1):73-82.
23. Liebich HM, Di Stefano C, Wixforth A, Schmid HR: Quantitation of urinary nucleosides by high-performance liquid chromatography. J Chromatogr A. 1997 Feb 28;763(1-2):193-7.