Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:52:27 UTC
Update Date2021-09-26 22:56:11 UTC
HMDB IDHMDB0246862
Secondary Accession NumbersNone
Metabolite Identification
Common Name5,6-Dihydroxyuracil
Description5,6-Dihydroxyuracil, also known as isodialuric acid or isodialate, belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 5,6-Dihydroxyuracil is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on 5,6-Dihydroxyuracil. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5,6-dihydroxyuracil is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5,6-Dihydroxyuracil is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
5,6-Dihydroxy-1,2,3,4-tetrahydropyrimidine-2,4-dioneChEBI
Isodialuric acidChEBI
IsodialateGenerator
Isodialic acidGenerator
5,6-Dihydroxy-2,4(1H,3H)pyrimidinedioneHMDB
Chemical FormulaC4H4N2O4
Average Molecular Weight144.086
Monoisotopic Molecular Weight144.017106617
IUPAC Name5,6-dihydroxy-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name5,6-dihydroxy-1,3-dihydropyrimidine-2,4-dione
CAS Registry NumberNot Available
SMILES
OC1=C(O)C(=O)NC(=O)N1
InChI Identifier
InChI=1S/C4H4N2O4/c7-1-2(8)5-4(10)6-3(1)9/h7H,(H3,5,6,8,9,10)
InChI KeyYFQOVSGFCVQZSW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentHydroxypyrimidines
Alternative Parents
Substituents
  • Pyrimidone
  • Hydroxypyrimidine
  • Hydropyrimidine
  • Vinylogous acid
  • Vinylogous amide
  • Heteroaromatic compound
  • Lactam
  • Urea
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.2ALOGPS
logP-0.97ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)5.21ChemAxon
pKa (Strongest Basic)-5.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area98.66 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity39.22 m³·mol⁻¹ChemAxon
Polarizability11.16 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+126.99330932474
DeepCCS[M-H]-123.88530932474
DeepCCS[M-2H]-160.97230932474
DeepCCS[M+Na]+135.85630932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.5157 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.06 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid571.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid354.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid73.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid241.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid69.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid282.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid295.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)327.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid626.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid205.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid771.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid212.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid249.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate677.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA232.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water304.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5,6-DihydroxyuracilOC1=C(O)C(=O)NC(=O)N12709.4Standard polar33892256
5,6-DihydroxyuracilOC1=C(O)C(=O)NC(=O)N11795.2Standard non polar33892256
5,6-DihydroxyuracilOC1=C(O)C(=O)NC(=O)N11920.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5,6-Dihydroxyuracil,3TMS,isomer #1C[Si](C)(C)OC1=C(O[Si](C)(C)C)N([Si](C)(C)C)C(=O)[NH]C1=O1822.9Semi standard non polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #1C[Si](C)(C)OC1=C(O[Si](C)(C)C)N([Si](C)(C)C)C(=O)[NH]C1=O1849.6Standard non polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #1C[Si](C)(C)OC1=C(O[Si](C)(C)C)N([Si](C)(C)C)C(=O)[NH]C1=O1875.2Standard polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #2C[Si](C)(C)OC1=C(O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)[NH]11769.0Semi standard non polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #2C[Si](C)(C)OC1=C(O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)[NH]11827.5Standard non polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #2C[Si](C)(C)OC1=C(O[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)[NH]11907.4Standard polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #3C[Si](C)(C)OC1=C(O)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C1965.5Semi standard non polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #3C[Si](C)(C)OC1=C(O)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C1822.6Standard non polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #3C[Si](C)(C)OC1=C(O)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C2008.1Standard polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #4C[Si](C)(C)OC1=C(O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1843.0Semi standard non polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #4C[Si](C)(C)OC1=C(O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1845.8Standard non polar33892256
5,6-Dihydroxyuracil,3TMS,isomer #4C[Si](C)(C)OC1=C(O)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1951.8Standard polar33892256
5,6-Dihydroxyuracil,4TMS,isomer #1C[Si](C)(C)OC1=C(O[Si](C)(C)C)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O2029.2Semi standard non polar33892256
5,6-Dihydroxyuracil,4TMS,isomer #1C[Si](C)(C)OC1=C(O[Si](C)(C)C)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1920.9Standard non polar33892256
5,6-Dihydroxyuracil,4TMS,isomer #1C[Si](C)(C)OC1=C(O[Si](C)(C)C)N([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1778.5Standard polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2393.7Semi standard non polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2535.2Standard non polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2263.2Standard polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)[NH]12352.6Semi standard non polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)[NH]12490.5Standard non polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)[NH]12275.8Standard polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC1=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2426.6Semi standard non polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC1=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2497.2Standard non polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC1=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2328.1Standard polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC1=C(O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2441.2Semi standard non polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC1=C(O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2506.3Standard non polar33892256
5,6-Dihydroxyuracil,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC1=C(O)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2296.7Standard polar33892256
5,6-Dihydroxyuracil,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2668.5Semi standard non polar33892256
5,6-Dihydroxyuracil,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2735.2Standard non polar33892256
5,6-Dihydroxyuracil,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2319.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-3900000000-8d356542d7b34ff644252021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dihydroxyuracil GC-MS (TBDMS_2_6) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dihydroxyuracil 10V, Positive-QTOFsplash10-0002-0900000000-6ee40f9b62ee45581cc42021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dihydroxyuracil 20V, Positive-QTOFsplash10-0fdw-9500000000-b53f57adbfae337112d52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dihydroxyuracil 40V, Positive-QTOFsplash10-05tf-9000000000-24aa187a6d98a37756b12021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dihydroxyuracil 10V, Negative-QTOFsplash10-0006-9600000000-d046640189ef270f969c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dihydroxyuracil 20V, Negative-QTOFsplash10-0006-9000000000-62bfe9c7670515fced242021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dihydroxyuracil 40V, Negative-QTOFsplash10-0006-9000000000-90726b17dc36e29c52992021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID61271
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound67956
PDB IDNot Available
ChEBI ID132197
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]