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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:02:43 UTC
HMDB IDHMDB00469
Secondary Accession NumbersNone
Metabolite Identification
Common Name5-Hydroxymethyluracil
Description5-Hydroxymethyluracil is an oxidation damage product derived from thymine or 5-methylcytosine. It is a product of thymine dioxygenase [EC 1.14.11.6]. (KEGG). Additional deamination products such as 5-hydroxymethyluracil are formed when cells are under oxidative stress that is induced either by oxidizing agents or by mitochondrial dysfunction. (PMID: 12361800 ).
Structure
Thumb
Synonyms
ValueSource
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
Chemical FormulaC5H6N2O3
Average Molecular Weight142.1127
Monoisotopic Molecular Weight142.037842068
IUPAC Name5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name5-hydroxymethyluracil
CAS Registry Number4433-40-3
SMILES
OCC1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C5H6N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1,8H,2H2,(H2,6,7,9,10)
InChI KeyInChIKey=JDBGXEHEIRGOBU-UHFFFAOYSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidones. These 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
  • Heteroaromatic compound
  • Vinylogous amide
  • Urea
  • Lactam
  • Azacycle
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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 Solubility44 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility14.0 mg/mLALOGPS
logP-1.3ALOGPS
logP-1.7ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)9.61ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area78.43 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.1 m3·mol-1ChemAxon
Polarizability12.34 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0a4i-0923000000-56a7dc66579bc2dd485bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00di-3900000000-5914a7f193ef00b46813View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0f89-9000000000-baed63743f1c3f212a8cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0pc0-9000000000-0ff7e6cec32d4f6a93ceView in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.12 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.0052 +/- 0.0026 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified88.0 +/- 8.0 uMAdult (>18 years old)Both
Solid tumors
details
BloodDetected and Quantified42.0 +/- 21.0 uMAdult (>18 years old)Both
Solid tumors
details
BloodDetected and Quantified15.0 +/- 2.0 uMAdult (>18 years old)Both
Solid tumors
details
BloodDetected and Quantified63.0 +/- 5.0 uMAdult (>18 years old)Both
Solid tumors
details
BloodDetected and Quantified33.0 +/- 4.0 uMAdult (>18 years old)Both
Solid tumors
details
UrineDetected and Quantified0.0062 +/- 0.0023 umol/mmol creatinineAdult (>18 years old)BothSmoking details
Associated Disorders and Diseases
Disease References
Smoking
  1. Chen HJ, Wu CF, Huang JL: Measurement of urinary excretion of 5-hydroxymethyluracil in human by GC/NICI/MS: correlation with cigarette smoking, urinary TBARS and etheno DNA adduct. Toxicol Lett. 2005 Mar 15;155(3):403-10. [15649624 ]
Thymidine treatment
  1. Leyva A, Schornagel JH, Kraal I, Wadman SK, Pinedo HM: Clinical and biochemical studies of high-dose thymidine treatment in patients with solid tumors. J Cancer Res Clin Oncol. 1984;107(3):211-6. [6736109 ]
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022061
KNApSAcK IDNot Available
Chemspider ID70544
KEGG Compound IDC03088
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
NuGOwiki LinkHMDB00469
Metagene LinkHMDB00469
METLIN ID5456
PubChem Compound78168
PDB IDHMU
ChEBI ID16964
References
Synthesis ReferenceAbbott, Mitchel Theodore. The cell-free synthesis of 5-hydroxymethyluracil. (1963), 140 pp
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Faure H, Coudray C, Mousseau M, Ducros V, Douki T, Bianchini F, Cadet J, Favier A: 5-Hydroxymethyluracil excretion, plasma TBARS and plasma antioxidant vitamins in adriamycin-treated patients. Free Radic Biol Med. 1996;20(7):979-83. [8743984 ]
  2. Baker D, Liu P, Burdzy A, Sowers LC: Characterization of the substrate specificity of a human 5-hydroxymethyluracil glycosylase activity. Chem Res Toxicol. 2002 Jan;15(1):33-9. [11800595 ]
  3. Loft S, Poulsen HE: Estimation of oxidative DNA damage in man from urinary excretion of repair products. Acta Biochim Pol. 1998;45(1):133-44. [9701506 ]
  4. Ito T, van Kuilenburg AB, Bootsma AH, Haasnoot AJ, van Cruchten A, Wada Y, van Gennip AH: Rapid screening of high-risk patients for disorders of purine and pyrimidine metabolism using HPLC-electrospray tandem mass spectrometry of liquid urine or urine-soaked filter paper strips. Clin Chem. 2000 Apr;46(4):445-52. [10759467 ]
  5. Kow YW: Repair of deaminated bases in DNA. Free Radic Biol Med. 2002 Oct 1;33(7):886-93. [12361800 ]