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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:02:45 UTC
HMDB IDHMDB00497
Secondary Accession NumbersNone
Metabolite Identification
Common Name5,6-Dihydrouridine
DescriptionDihydrouridine is a pyrimidine which is the result of adding two hydrogen atoms to a uridine. Dihydrouridine is found only in tRNA molecules. An inhibitor of nucleotide metabolism.
Structure
Thumb
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
Chemical FormulaC9H14N2O6
Average Molecular Weight246.2173
Monoisotopic Molecular Weight246.08518619
IUPAC Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,3-diazinane-2,4-dione
Traditional Namedihydrouridine
CAS Registry Number5627-05-4
SMILES
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O
InChI Identifier
InChI=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 KeyInChIKey=ZPTBLXKRQACLCR-XVFCMESISA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as glycosylamines. These 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 ClassOrganooxygen compounds
ClassCarbohydrates and carbohydrate conjugates
Sub ClassGlycosyl compounds
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • N-glycosyl compound
  • Ureide
  • Pyrimidone
  • Pyrimidine
  • Monosaccharide
  • 1,3-diazinane
  • Oxolane
  • Urea
  • Tertiary amine
  • Secondary alcohol
  • Carboxamide group
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Primary alcohol
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility231.0 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity52.34 m3·mol-1ChemAxon
Polarizability22.98 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot Available
Normal
  • Not Applicable
details
UrineDetected and Quantified6.37 +/- 1.38 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified7.03 +/- 1.31 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified5.83 +/- 1.22 umol/mmol creatinineAdult (>18 years old)MaleNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022076
KNApSAcK IDNot Available
Chemspider ID85115
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDihydrouridine
NuGOwiki LinkHMDB00497
Metagene LinkHMDB00497
METLIN ID5483
PubChem Compound94312
PDB IDNot Available
ChEBI ID23774
References
Synthesis ReferenceCerutti, 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.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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. [9129323 ]
  2. 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. [2817393 ]
  3. 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. [8299222 ]

Enzymes

General function:
Involved in catalytic activity
Specific function:
Dihydrouridine synthase. Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Gene Name:
DUS2L
Uniprot ID:
Q9NX74
Molecular weight:
55049.8
General function:
Involved in catalytic activity
Specific function:
Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Gene Name:
DUS1L
Uniprot ID:
Q6P1R4
Molecular weight:
53230.0
General function:
Involved in catalytic activity
Specific function:
Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Gene Name:
DUS3L
Uniprot ID:
Q96G46
Molecular weight:
72593.3
General function:
Involved in catalytic activity
Specific function:
Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Gene Name:
DUS4L
Uniprot ID:
O95620
Molecular weight:
35816.2
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
PP35
Uniprot ID:
A4D0R5
Molecular weight:
35816.2