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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:30 UTC
Update Date2017-12-07 01:46:49 UTC
HMDB IDHMDB0001983
Secondary Accession Numbers
  • HMDB01983
Metabolite Identification
Common Name5'-Deoxyadenosine
Description5'-Deoxyadenosine is an oxidized nucleoside found in the urine of normal subjects. Oxidized nucleosides represent excellent biomarkers for determining the extent of damage in genetic material, which has long been of interest in understanding the mechanism of aging, neurodegenerative diseases, and carcinogenesis. (PMID 15116424 ). The normal form of deoxyadenosine used in DNA synthesis and repair is 2'-deoxyadenosine where the hydroxyl group (-OH) is at the 2' position of its ribose sugar moiety. 5'-deoxyadenosine has its hydroxyl group at the 5' position of the ribose sugar.
Structure
Thumb
Synonyms
ValueSource
5'-Deoxy-adenosineHMDB
Chemical FormulaC10H13N5O3
Average Molecular Weight251.2419
Monoisotopic Molecular Weight251.101839307
IUPAC Name(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-methyloxolane-3,4-diol
Traditional Name5'-deoxyadenosine
CAS Registry Number4754-39-6
SMILES
C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12
InChI Identifier
InChI=1S/C10H13N5O3/c1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15/h2-4,6-7,10,16-17H,1H3,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
InChI KeyXGYIMTFOTBMPFP-KQYNXXCUSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub Class5'-deoxyribonucleosides
Direct Parent5'-deoxyribonucleosides
Alternative Parents
Substituents
  • 5'-deoxyribonucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • N-substituted imidazole
  • Primary aromatic amine
  • Imidolactam
  • Pyrimidine
  • Oxolane
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • 1,2-diol
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Alcohol
  • Organic oxygen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Amine
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

  Cell and elements:

Source:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point213.0 - 214.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility9.88 g/LALOGPS
logP-0.52ALOGPS
logP-1ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)12.48ChemAxon
pKa (Strongest Basic)4.99ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area119.31 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity61.65 m³·mol⁻¹ChemAxon
Polarizability24.26 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05dl-9640000000-ee63a0f0a804463c5d3bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00wi-9757000000-b8ba57885a813934cb02View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-001i-0910000000-e2fb3e0d3b85b88eaf9fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0udi-0490000000-2d56a55a6dcc84b79cbbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-0900000000-bc60a46e6751486debe1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-1900000000-aa5e98075bbd2c17e6e9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-3900000000-97cb5373efd784d8bc46View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-5900000000-fc447cfd2476fd6fc248View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-000i-0900000000-decd8c6638992a36e5c1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-000i-0900000000-bcb75d9aef2d7b125ff7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0940000000-20bada9b7c3914ebd835View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-e218ae45a376f2d35bffView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014r-3900000000-4803d4734d389249e54bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ue9-0790000000-e9f6fee027d381974116View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-0900000000-f8cfbe38fa6d8b9a9b3eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05o0-4900000000-b861ad521faa95835ac1View in MoNA
Biological Properties
Cellular Locations
  • Extracellular
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
NameSMPDB/PathwhizKEGG
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not Quantified Not AvailableNot Available
Normal
    details
    UrineDetected and Quantified0.078 (0.054-0.102) umol/mmol creatinineAdult (>18 years old)BothNormal details
    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 IDFDB022781
    KNApSAcK IDNot Available
    Chemspider ID388325
    KEGG Compound IDC05198
    BioCyc IDCH33ADO
    BiGG ID45324
    Wikipedia LinkNot Available
    METLIN IDNot Available
    PubChem Compound439182
    PDB ID5AD
    ChEBI ID17319
    References
    Synthesis ReferenceLerner, Leon M. An improved preparation of 5'-deoxyadenosine by coupling methods. Carbohydrate Research (1988), 184 250-3.
    Material Safety Data Sheet (MSDS)Download (PDF)
    General References
    1. Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. [PubMed:15116424 ]

    Enzymes

    General function:
    Involved in catalytic activity
    Specific function:
    Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives (By similarity).
    Gene Name:
    LIAS
    Uniprot ID:
    O43766
    Molecular weight:
    41910.695
    Reactions
    Protein N(6)-(octanoyl)lysine + Hydrogen sulfide + S-Adenosylmethionine → protein N(6)-(lipoyl)lysine + L-Methionine + 5'-Deoxyadenosinedetails
    Protein N6-(octanoyl)lysine + Sulfur donor + S-Adenosylmethionine → Protein N6-(lipoyl)lysine + L-Methionine + 5'-Deoxyadenosinedetails
    Octanoyl-[acp] + Sulfur donor + S-Adenosylmethionine → Lipoyl-[acp] + L-Methionine + 5'-Deoxyadenosinedetails