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Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-02-26 21:22:06 UTC
HMDB IDHMDB0000366
Secondary Accession Numbers
  • HMDB00366
Metabolite Identification
Common Name2-Deoxyribonic acid
Description2-Deoxyribonic acid is the acid form of deoxyribonate (interconvertible with 2-Deoxyribonolactone), produced as part of bistranded lesions by DNA damaging agents, including the antitumor agents bleomycin and the neocarzinostatin chromophore (PMID 2523732 ). This lesion is also produced by ionizing radiation, organometallic oxidants, and is a metastable intermediate in DNA damage mediated by copper phenanthroline nucleases, and is also formed under anaerobic conditions in the presence of the radiosensitizing agent tirapazamine. (PMID 12600212 ), and it has been found in normal human biofluids (PMID 2925825 , 3829393 , 6725493 , 7228943 ).
Structure
Data?1582752126
Synonyms
ValueSource
2-DeoxyribonateGenerator
2-Deoxy-D-ribonateHMDB
2-Deoxy-D-ribonic acidHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name(3S,4R)-3,4,5-trihydroxypentanoic acid
Traditional Name(3S,4R)-3,4,5-trihydroxypentanoic acid
CAS Registry Number29625-75-0
SMILES
OC[C@@H](O)[C@@H](O)CC(O)=O
InChI Identifier
InChI=1S/C5H10O5/c6-2-4(8)3(7)1-5(9)10/h3-4,6-8H,1-2H2,(H,9,10)/t3-,4+/m0/s1
InChI KeyVBUWJOHKCBQXNU-IUYQGCFVSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassBeta hydroxy acids and derivatives
Direct ParentBeta hydroxy acids and derivatives
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Short-chain hydroxy acid
  • Fatty acid
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Polyol
  • Organooxygen compound
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Primary alcohol
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Source:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility511 g/LALOGPS
logP-2ALOGPS
logP-2.1ChemAxon
logS0.53ALOGPS
pKa (Strongest Acidic)4.03ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.97 m³·mol⁻¹ChemAxon
Polarizability13.51 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-06sc-9000000000-c78de6841f3acf1fa76bSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-00g0-9027200000-adc32665fe9b412fb0fbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-1900000000-abab4e4ee07915ad25dfSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-07cu-9700000000-56ec7d5976e902370580Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-06xx-9000000000-cb82a1f13b50d91492bdSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052b-3900000000-0b54ad95ab8a0e82a5a0Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4r-9300000000-1190b2589b795883f41cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000000000-6a9184456a482fb916e1Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not Quantified Adult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021985
KNApSAcK IDNot Available
Chemspider ID9703151
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5355
PubChem Compound11528367
PDB IDNot Available
ChEBI ID86350
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceYang, Byung Yun; Montgomery, Rex. Alkaline degradation of fructofuranosides. Carbohydrate Research (1996), 280(1), 47-57.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Davies M, Adams PH, Berry JL, Lumb GA, Klimiuk PS, Mawer EB, Wain D: Familial hypocalciuric hypercalcaemia: observations on vitamin D metabolism and parathyroid function. Acta Endocrinol (Copenh). 1983 Oct;104(2):210-5. [PubMed:6314724 ]
  2. Kappen LS, Goldberg IH: Identification of 2-deoxyribonolactone at the site of neocarzinostatin-induced cytosine release in the sequence d(AGC). Biochemistry. 1989 Feb 7;28(3):1027-32. [PubMed:2523732 ]
  3. Kroeger KM, Hashimoto M, Kow YW, Greenberg MM: Cross-linking of 2-deoxyribonolactone and its beta-elimination product by base excision repair enzymes. Biochemistry. 2003 Mar 4;42(8):2449-55. [PubMed:12600212 ]
  4. Lefevere MF, Verhaeghe BJ, Declerck DH, Van Bocxlaer JF, De Leenheer AP, De Sagher RM: Metabolic profiling of urinary organic acids by single and multicolumn capillary gas chromatography. J Chromatogr Sci. 1989 Jan;27(1):23-9. [PubMed:2925825 ]
  5. Chamberlin BA, Sweeley CC: Metabolic profiles of urinary organic acids recovered from absorbent filter paper. Clin Chem. 1987 Apr;33(4):572-6. [PubMed:3829393 ]
  6. Tuchman M, Bowers LD, Fregien KD, Crippin PJ, Krivit W: Capillary gas chromatographic separation of urinary organic acids. Retention indices of 101 urinary acids on a 5% phenylmethyl silicone capillary column. J Chromatogr Sci. 1984 May;22(5):198-202. [PubMed:6725493 ]
  7. Sims P, Truscott R, Halpern B: Improved procedure for the anion-exchange isolation of urinary organic acids. J Chromatogr. 1981 Mar 13;222(3):337-44. [PubMed:7228943 ]