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Record Information
Version3.6
Creation Date2006-05-22 14:17:30 UTC
Update Date2016-02-11 01:05:11 UTC
HMDB IDHMDB01983
Secondary Accession NumbersNone
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
CH3AdoMetaCyc
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 KeyInChIKey=XGYIMTFOTBMPFP-KQYNXXCUSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as glycosylamines. These are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).
KingdomOrganic compounds
Super ClassOrganooxygen compounds
ClassCarbohydrates and carbohydrate conjugates
Sub ClassGlycosyl compounds
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • N-glycosyl compound
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Aminopyrimidine
  • Imidolactam
  • Pyrimidine
  • Primary aromatic amine
  • N-substituted imidazole
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Extracellular
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 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity61.65 m3·mol-1ChemAxon
Polarizability24.26 Å3ChemAxon
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-MSNot Available
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
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot Available
Normal
  • Not Applicable
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
NuGOwiki LinkHMDB01983
Metagene LinkHMDB01983
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. [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