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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:02:35 UTC
HMDB IDHMDB00366
Secondary Accession NumbersNone
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
Thumb
Synonyms
ValueSource
2-Deoxy-D-ribonateHMDB
2-Deoxy-D-ribonic acidHMDB
2-DeoxyribonateHMDB
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 KeyInChIKey=VBUWJOHKCBQXNU-IUYQGCFVSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Beta-hydroxy acid
  • Hydroxy acid
  • Secondary alcohol
  • Polyol
  • 1,2-diol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
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 Solubility511.0 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.97 m3·mol-1ChemAxon
Polarizability13.51 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular LocationsNot Available
Biofluid LocationsNot Available
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB021985
KNApSAcK IDNot Available
Chemspider ID9703151
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
NuGOwiki LinkHMDB00366
Metagene LinkHMDB00366
METLIN ID5355
PubChem Compound11528367
PDB IDNot Available
ChEBI 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. [6314724 ]
  2. 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. [2925825 ]
  3. Chamberlin BA, Sweeley CC: Metabolic profiles of urinary organic acids recovered from absorbent filter paper. Clin Chem. 1987 Apr;33(4):572-6. [3829393 ]
  4. 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. [2523732 ]
  5. 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. [12600212 ]
  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. [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. [7228943 ]