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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 22:52:29 UTC
Update Date2021-09-23 22:52:30 UTC
HMDB IDHMDB0303045
Secondary Accession NumbersNone
Metabolite Identification
Common Name5-Hydroxyuracil
Description5-hydroxyuracil, also known as dihydropyrimidine-2,4,5(3h)-trione or isobarbituric acid, is a member of the class of compounds known as hydroxypyrimidines. Hydroxypyrimidines 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-hydroxyuracil is slightly soluble (in water) and a very weakly acidic compound (based on its pKa). 5-hydroxyuracil can be found in broad bean, which makes 5-hydroxyuracil a potential biomarker for the consumption of this food product. 5-hydroxyuracil is an oxidized form of cytosine that is produced by the oxidative deamination of cytosines by reactive oxygen species. It does not distort the DNA molecule and is bypassed by replicative DNA polymerases. It can miscode for adenine and is potentially mutagenic .
Structure
Thumb
Synonyms
ValueSource
Dihydropyrimidine-2,4,5(3H)-trioneChEBI
Isobarbituric acidChEBI
IsobarbitateGenerator
Isobarbitic acidGenerator
Chemical FormulaC4H4N2O3
Average Molecular Weight128.0862
Monoisotopic Molecular Weight128.022192004
IUPAC Name5-hydroxy-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name5-hydroxyuracil
CAS Registry NumberNot Available
SMILES
OC1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C4H4N2O3/c7-2-1-5-4(9)6-3(2)8/h1,7H,(H2,5,6,8,9)
InChI KeyOFJNVANOCZHTMW-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
  • Hydroxypyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Polyol
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot 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-1.4ALOGPS
logP-1.1ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)8.8ChemAxon
pKa (Strongest Basic)-4.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area78.43 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity27.94 m³·mol⁻¹ChemAxon
Polarizability10.27 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
AllCCS[M+H]+127.37532859911
AllCCS[M+H-H2O]+122.58632859911
AllCCS[M+Na]+133.13532859911
AllCCS[M+NH4]+131.84532859911
AllCCS[M-H]-120.65232859911
AllCCS[M+Na-2H]-122.72232859911
AllCCS[M+HCOO]-125.03332859911
DeepCCS[M+H]+119.92130932474
DeepCCS[M-H]-116.91330932474
DeepCCS[M-2H]-153.28630932474
DeepCCS[M+Na]+128.47930932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-Hydroxyuracil,2TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)[NH]C1=O1729.7Semi standard non polar33892256
5-Hydroxyuracil,2TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)[NH]C1=O1753.8Standard non polar33892256
5-Hydroxyuracil,2TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)[NH]C1=O1982.2Standard polar33892256
5-Hydroxyuracil,2TMS,isomer #2C[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C)C1=O1672.5Semi standard non polar33892256
5-Hydroxyuracil,2TMS,isomer #2C[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C)C1=O1732.7Standard non polar33892256
5-Hydroxyuracil,2TMS,isomer #2C[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C)C1=O1907.1Standard polar33892256
5-Hydroxyuracil,2TMS,isomer #3C[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C)C1=O1693.8Semi standard non polar33892256
5-Hydroxyuracil,2TMS,isomer #3C[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C)C1=O1741.7Standard non polar33892256
5-Hydroxyuracil,2TMS,isomer #3C[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C)C1=O2020.2Standard polar33892256
5-Hydroxyuracil,3TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1858.3Semi standard non polar33892256
5-Hydroxyuracil,3TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1823.9Standard non polar33892256
5-Hydroxyuracil,3TMS,isomer #1C[Si](C)(C)OC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1836.9Standard polar33892256
5-Hydroxyuracil,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2198.0Semi standard non polar33892256
5-Hydroxyuracil,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2193.1Standard non polar33892256
5-Hydroxyuracil,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O2172.6Standard polar33892256
5-Hydroxyuracil,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O2127.8Semi standard non polar33892256
5-Hydroxyuracil,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O2157.6Standard non polar33892256
5-Hydroxyuracil,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O2096.5Standard polar33892256
5-Hydroxyuracil,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2134.8Semi standard non polar33892256
5-Hydroxyuracil,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2160.6Standard non polar33892256
5-Hydroxyuracil,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)N1C=C(O)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2151.1Standard polar33892256
5-Hydroxyuracil,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2398.9Semi standard non polar33892256
5-Hydroxyuracil,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2456.2Standard non polar33892256
5-Hydroxyuracil,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2180.3Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 10V, Positive-QTOFsplash10-004i-2900000000-7c98db209af74a35673f2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 20V, Positive-QTOFsplash10-06vr-9700000000-5f609d5f41d3ad58ca812016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 40V, Positive-QTOFsplash10-0ab9-9000000000-e8b1bac36c23b484e8fc2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 10V, Negative-QTOFsplash10-004l-9800000000-47afce14571a38f0a3132016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 20V, Negative-QTOFsplash10-0006-9100000000-b393d7ba3fdf523f21a52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 40V, Negative-QTOFsplash10-0006-9000000000-ca85a1bf1d20542f3ae52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 10V, Positive-QTOFsplash10-004i-0900000000-29b0b53134d035b235ae2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 20V, Positive-QTOFsplash10-004i-9800000000-82c2f9c5476ae42d70ba2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 40V, Positive-QTOFsplash10-0aou-9000000000-c010103cfa38919d03212021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 10V, Negative-QTOFsplash10-004l-6900000000-c1f4383276e3eda60a682021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 20V, Negative-QTOFsplash10-0006-9000000000-b21221b06476df9dd12b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxyuracil 40V, Negative-QTOFsplash10-0006-9000000000-90726b17dc36e29c52992021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB007481
KNApSAcK IDNot Available
Chemspider ID66014
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID29115
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 ReferencesNot Available