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Identification
YMDB IDYMDB00150
Name5'-Deoxyadenosine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description5'-Deoxyadenosine, also known as 5'-dado nucleoside, belongs to the class of organic compounds 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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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. 5'-Deoxyadenosine is a strong basic compound (based on its pKa). 5'-Deoxyadenosine exists in all living species, ranging from bacteria to humans.
Structure
Thumb
Synonyms
  • 5'-deoxy-adenosine
  • 5'-DAdo nucleoside
CAS number4754-39-6
WeightAverage: 251.2419
Monoisotopic: 251.101839307
InChI KeyXGYIMTFOTBMPFP-KQYNXXCUSA-N
InChIInChI=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
IUPAC Name(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-methyloxolane-3,4-diol
Traditional IUPAC Name5'-deoxyadenosine
Chemical FormulaC10H13N5O3
SMILES[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])[H])[C@@]1([H])O[H])N1C([H])=NC2=C1N=C([H])N=C2N([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds 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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
Class5'-deoxyribonucleosides
Sub ClassNot Available
Direct Parent5'-deoxyribonucleosides
Alternative Parents
Substituents
  • 5'-deoxyribonucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Aminopyrimidine
  • Imidolactam
  • Pyrimidine
  • N-substituted imidazole
  • Azole
  • Heteroaromatic compound
  • Imidazole
  • Tetrahydrofuran
  • 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
Physical Properties
StateSolid
Charge0
Melting point213.0-214.5 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility9.88 g/LALOGPS
logP-0.52ALOGPS
logP-1ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)12.48ChemAxon
pKa (Strongest Basic)3.92ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area119.31 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity61.65 m³·mol⁻¹ChemAxon
Polarizability24.3 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm, Extracellular
Organoleptic PropertiesNot Available
SMPDB Pathways
Biotin BiosynthesisPW002380 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
Dethiobiotin + S-Adenosyl-L-methionine + Reduced ferredoxin + a sulfurated [sulfur carrier]  → Biotin + L-Methionine + 5'-Deoxyadenosine + an unsulfurated [sulfur carrier] + Oxidized ferredoxin
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05dl-9640000000-ee63a0f0a804463c5d3bJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00wi-9757000000-b8ba57885a813934cb02JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-001i-0910000000-e2fb3e0d3b85b88eaf9fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0udi-0490000000-2d56a55a6dcc84b79cbbJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-0900000000-bc60a46e6751486debe1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-1900000000-aa5e98075bbd2c17e6e9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-3900000000-97cb5373efd784d8bc46JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-5900000000-fc447cfd2476fd6fc248JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-000i-0900000000-decd8c6638992a36e5c1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-000i-0900000000-bcb75d9aef2d7b125ff7JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0940000000-20bada9b7c3914ebd835JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-e218ae45a376f2d35bffJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014r-3900000000-4803d4734d389249e54bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ue9-0790000000-e9f6fee027d381974116JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-0900000000-f8cfbe38fa6d8b9a9b3eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05o0-4900000000-b861ad521faa95835ac1JSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Synthesis Reference:Lerner, Leon M. An improved preparation of 5'-deoxyadenosine by coupling methods. Carbohydrate Research (1988), 184 250-3.
External Links:
ResourceLink
CHEBI ID17319
HMDB IDHMDB01983
Pubchem Compound ID439182
Kegg IDC05198
ChemSpider ID388325
FOODB IDFDB022781
WikipediaDeoxyadenosine
BioCyc IDCH33ADO

Enzymes

General function:
Involved in catalytic activity
Specific function:
Dethiobiotin + sulfur + 2 S-adenosyl-L- methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine
Gene Name:
BIO2
Uniprot ID:
P32451
Molecular weight:
41883.80078
Reactions
Dethiobiotin + sulfur + 2 S-adenosyl-L-methionine → biotin + 2 L-methionine + 2 5'-deoxyadenosine.
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 (Probable)
Gene Name:
LIP5
Uniprot ID:
P32875
Molecular weight:
46246.80078
Reactions
Protein N(6)-(octanoyl)lysine + 2 sulfur + 2 S-adenosyl-L-methionine → protein N(6)-(lipoyl)lysine + 2 L-methionine + 2 5'-deoxyadenosine.