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Human Metabolome Database Version 3.5

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Showing metabocard for 5-Hydroxymethyluracil (HMDB00469)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:08:38 -0700
HMDB ID HMDB00469
Secondary Accession Numbers None
Metabolite Identification
Common Name 5-Hydroxymethyluracil
Description 5-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 Link_out).
Structure Thumb
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 5-(Hydroxymethyl)-1,3-dihydropyrimidine-2,4-dione
  2. 5-(Hydroxymethyl)-2,4(1H,3H)-pyrimidinedione
  3. 5-(Hydroxymethyl)uracil
  4. 5-Hydroxymethyluracil
  5. a-Hydroxythymine
  6. alpha-Hydroxythymine
Chemical Formula C5H6N2O3
Average Molecular Weight 142.1127
Monoisotopic Molecular Weight 142.037842068
IUPAC Name 5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name 5-hydroxymethyluracil
CAS Registry Number 4433-40-3
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 Key JDBGXEHEIRGOBU-UHFFFAOYSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Aromatic Heteromonocyclic Compounds
Class Diazines
Sub Class Pyrimidines and Pyrimidine Derivatives
Other Descriptors
  • Pyrimidines and Pyrimidine Derivatives
  • a small molecule(Cyc)
  • primary alcohol(ChEBI)
Substituents
  • Hydropyrimidine
  • Primary Alcohol
Direct Parent Pyrimidones
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction Not Available
Application Not Available
Cellular locations
  • Cytoplasm
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility 44 mg/mL Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 14 g/L ALOGPS
LogP -1.31 ALOGPS
LogP -1.7 ChemAxon
LogS -1.01 ALOGPS
pKa (strongest acidic) 9.61 ChemAxon
pKa (strongest basic) -2.8 ChemAxon
Hydrogen Acceptor Count 3 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 78.43 A2 ChemAxon
Rotatable Bond Count 1 ChemAxon
Refractivity 32.1 ChemAxon
Polarizability 12.34 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies )
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue Location Not Available
Pathways Not Available
Normal Concentrations
Biofluid Status Value Age Sex Condition Comments
Urine Detected and Quantified
Article_icon
0.12 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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0.0062 +/- 0.0023 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
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0.0052 +/- 0.0026 umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Comments
Blood Detected and Quantified
Article_icon
88.0 +/- 8.0 uM Adult (>18 years old) Both Thymidine treatment Result for one of ten patients with infusion of...
Blood Detected and Quantified
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42.0 +/- 21.0 uM Adult (>18 years old) Both Thymidine treatment Result for one of ten patients with infusion of...
Blood Detected and Quantified
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15.0 +/- 2.0 uM Adult (>18 years old) Both Thymidine treatment Result for one of ten patients with infusion of...
Blood Detected and Quantified
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63.0 +/- 5.0 uM Adult (>18 years old) Both Thymidine treatment Result for one of ten patients with infusion of...
Blood Detected and Quantified
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33.0 +/- 4.0 uM Adult (>18 years old) Both Thymidine treatment Result for one of ten patients with infusion of...
Associated Disorders and Diseases
Disease References
Thymidine treatment
  • 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 Link_out
    Smoking
    • 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 Link_out
      Associated OMIM IDs None
      DrugBank ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB022061
      KNApSAcK ID Not Available
      Chemspider ID 70544 Link_out
      KEGG Compound ID C03088 Link_out
      BioCyc ID Not Available
      BiGG ID Not Available
      Wikipedia Link Not Available
      NuGOwiki Link HMDB00469 Link_out
      Metagene Link HMDB00469 Link_out
      METLIN ID 5456 Link_out
      PubChem Compound 78168 Link_out
      PDB ID HMU Link_out
      ChEBI ID 16964 Link_out
      References
      Synthesis Reference Abbott, 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 Link_out
      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 Link_out
      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 Link_out
      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 Link_out