Record Information
Version1.0
Creation date2011-09-21 00:07:48 UTC
Update date2019-11-26 03:21:01 UTC
Primary IDFDB022061
Secondary Accession NumbersNot Available
Chemical Information
FooDB Name5-Hydroxymethyluracil
Description5-Hydroxymethyluracil, also known as a-hydroxythymine, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 5-Hydroxymethyluracil has been detected, but not quantified in, several different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), domestic pigs (Sus scrofa domestica), and milk (cow). This could make 5-hydroxymethyluracil a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 5-Hydroxymethyluracil.
CAS Number4433-40-3
Structure
Thumb
Synonyms
SynonymSource
5-(Hydroxymethyl)-2,4(1H,3H)-pyrimidinedioneChEBI
5-(Hydroxymethyl)uracilChEBI
5-HYDROXYMETHYL uracilChEBI
5-(Hydroxymethyl)-1,3-dihydropyrimidine-2,4-dioneHMDB
a-HydroxythymineHMDB
alpha-HydroxythymineHMDB
HydroxymethyluracilHMDB
5-Hydroxymethyluracilhmdb
Predicted Properties
PropertyValueSource
Water Solubility14 g/LALOGPS
logP-1.3ALOGPS
logP-1.7ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)8.68ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area78.43 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.1 m³·mol⁻¹ChemAxon
Polarizability12.34 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC5H6N2O3
IUPAC name5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione
InChI IdentifierInChI=1S/C5H6N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1,8H,2H2,(H2,6,7,9,10)
InChI KeyJDBGXEHEIRGOBU-UHFFFAOYSA-N
Isomeric SMILESOCC1=CNC(=O)NC1=O
Average Molecular Weight142.1127
Monoisotopic Molecular Weight142.037842068
Classification
Description Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. 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 ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • Vinylogous amide
  • Heteroaromatic compound
  • Lactam
  • Urea
  • Azacycle
  • Alcohol
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Organic oxide
  • Organopnictogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Disposition

Source:

Biological location:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
GC-MS5-Hydroxymethyluracil, non-derivatized, GC-MS Spectrumsplash10-0a4i-0923000000-56a7dc66579bc2dd485bSpectrum
GC-MS5-Hydroxymethyluracil, non-derivatized, GC-MS Spectrumsplash10-0a4i-0923000000-56a7dc66579bc2dd485bSpectrum
Predicted GC-MS5-Hydroxymethyluracil, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-03kc-4900000000-1cac35d0ba0cca9e8da8Spectrum
Predicted GC-MS5-Hydroxymethyluracil, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-00di-5910000000-e4ecb5b2c252b1dd98a6Spectrum
Predicted GC-MS5-Hydroxymethyluracil, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MS5-Hydroxymethyluracil, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MS5-Hydroxymethyluracil, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MS5-Hydroxymethyluracil, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MS5-Hydroxymethyluracil, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MS5-Hydroxymethyluracil, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MS5-Hydroxymethyluracil, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00di-3900000000-5914a7f193ef00b468132012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0f89-9000000000-baed63743f1c3f212a8c2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0pc0-9000000000-0ff7e6cec32d4f6a93ce2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - , negativesplash10-0006-1900000000-c15a268f199a45782f942017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0006-9200000000-37d9ec4a1e994196876b2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-743c2de03cb5f65bb4582021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0006-1900000000-9692a096d1a7d0bb32c82021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0006-7900000000-ebcc62da3f6c16c368f92021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004l-0900000000-4db52d8921bc6b9e27d92017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-6900000000-74ddd3dbfd8e6a457bee2017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000t-9100000000-b418e2767863592cb8de2017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-2900000000-5c173dfa10b778d98c522017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9500000000-b46a4f1e0f9872c639de2017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-6613bb83bb842d70dfc02017-09-01View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-c9b85bee66bc9b6f7fa52021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-fb2fe160d3fd7a32fbfc2021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-05fr-9000000000-0e50a0012c8e06917b1a2021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-006x-1900000000-972ab29c67e5ac9b71022021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00dl-8900000000-e306682075b170218ba82021-09-24View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-e3c2901699c5071255a02021-09-24View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
ChemSpider ID70544
ChEMBL IDNot Available
KEGG Compound IDC03088
Pubchem Compound ID78168
Pubchem Substance IDNot Available
ChEBI ID16964
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB00469
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDHMU
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference