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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-07 01:17:07 UTC
HMDB IDHMDB0000469
Secondary Accession Numbers
  • HMDB00469
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
HydroxymethyluracilMeSH
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 KeyJDBGXEHEIRGOBU-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
  • 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:

  Health condition:

Disposition

Biological location:

  Subcellular:

  Biofluid and excreta:

Source:

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 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.1 m³·mol⁻¹ChemAxon
Polarizability12.34 ųChemAxon
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) (Non-derivatized)splash10-0a4i-0923000000-56a7dc66579bc2dd485bView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4i-0923000000-56a7dc66579bc2dd485bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03kc-4900000000-1cac35d0ba0cca9e8da8View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00di-5910000000-e4ecb5b2c252b1dd98a6View 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
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0006-1900000000-c15a268f199a45782f94View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004l-0900000000-4db52d8921bc6b9e27d9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-6900000000-74ddd3dbfd8e6a457beeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000t-9100000000-b418e2767863592cb8deView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-2900000000-5c173dfa10b778d98c52View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9500000000-b46a4f1e0f9872c639deView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-6613bb83bb842d70dfc0View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
NameSMPDB/PathwhizKEGG
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. [PubMed: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. [PubMed:6736109 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022061
KNApSAcK IDNot Available
Chemspider ID70544
KEGG Compound IDC03088
BioCyc IDCPD-254
BiGG IDNot Available
Wikipedia LinkNot Available
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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:10759467 ]
  5. Kow YW: Repair of deaminated bases in DNA. Free Radic Biol Med. 2002 Oct 1;33(7):886-93. [PubMed:12361800 ]