You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-08-16 03:20:44 UTC
HMDB IDHMDB0000497
Secondary Accession Numbers
  • HMDB00497
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
DihydrouridineHMDB
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 KeyZPTBLXKRQACLCR-XVFCMESISA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities 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).
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic oxygen compounds
Sub ClassOrganooxygen compounds
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • N-glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Ureide
  • Hydropyrimidine
  • 1,2,5,6-tetrahydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Oxolane
  • Secondary alcohol
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Hydrocarbon derivative
  • Organic oxide
  • Organic nitrogen compound
  • Primary alcohol
  • Organopnictogen compound
  • Organonitrogen compound
  • Carbonyl group
  • 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 Quantified Not AvailableNot Available
Normal
    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 LinkHMDB0000497
    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. [PubMed: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. [PubMed: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. [PubMed: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