5'-Deoxyadenosine (PAMDB001583)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001583
Identification
Name: 5'-Deoxyadenosine
Description:5'-Deoxyadenosine is an abnormal form of deoxyadenosine derived from S-adenosylmethionine. 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. 5'-deoxyadenosine is a substrate for 5'-methylthioadenosine phosphorylase. It is also a product of the degradation/conversion of S-adenosyl-methionine by the enzymes: 2-iminoacetate synthase, biotin synthase, lopoyl synthase and pyruvate-formate lyase activating enzyme
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 5'-Deoxy-adenosine
  • 5'-Deoxyadenosine
  • CH3Ado
  • CH3Ado
Chemical Formula: C10H13N5O3
Average Molecular Weight: 251.2419
Monoisotopic Molecular Weight: 251.101839307
InChI Key: XGYIMTFOTBMPFP-KQYNXXCUSA-N
InChI: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
CAS number: 4754-39-6
IUPAC Name:(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-methyloxolane-3,4-diol
Traditional IUPAC Name: 5'-deoxyadenosine
SMILES:C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12
Chemical Taxonomy
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).
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassGlycosyl compounds
Direct Parent Glycosylamines
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 Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 213.0-214.5 °C
Experimental Properties:
PropertyValueSource
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
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
5'-Deoxyadenosine + Water > 5'-Deoxyribose + Adenine
[4Fe-4S] iron-sulfur cluster + 2 S-Adenosylmethionine + Hydrogen ion + NAD + octanoate (protein bound) > [2Fe-2S] iron-sulfur cluster +2 5'-Deoxyadenosine +2 Iron + lipoate (protein bound) +2 L-Methionine + NADH
[2Fe-2S] iron-sulfur cluster + S-Adenosylmethionine + Dethiobiotin > [2Fe-1S] desulfurated iron-sulfur cluster + Biotin + 5'-Deoxyadenosine + Hydrogen ion + L-Methionine
2 S-Adenosylmethionine + Coproporphyrin III <>2 Carbon dioxide +2 5'-Deoxyadenosine +2 L-Methionine + Protoporphyrinogen IX
S-Adenosylmethionine + NADPH + L-Tyrosine > p-Cresol + 5'-Deoxyadenosine + Dehydroglycine + Hydrogen ion + L-Methionine + NADP
Dethiobiotin + Sulfur donor + 2 S-Adenosylmethionine + 2 e- + 2 Hydrogen ion <> Biotin +2 L-Methionine +2 5'-Deoxyadenosine
4-Amino-5-hydroxymethyl-2-methylpyrimidine + S-Adenosylmethionine <> 5-Aminoimidazole ribonucleotide + 4-Amino-2-methyl-5-phosphomethylpyrimidine + 5'-Deoxyadenosine + L-Methionine + Formic acid + CO
Protein N6-(octanoyl)lysine + 2 Sulfur donor + 2 S-Adenosylmethionine + Protein N6-(octanoyl)lysine <> Protein N6-(lipoyl)lysine +2 L-Methionine +2 5'-Deoxyadenosine + Protein N6-(lipoyl)lysine
Octanoyl-[acp] + 2 Sulfur donor + 2 S-Adenosylmethionine <> Lipoyl-[acp] +2 L-Methionine +2 5'-Deoxyadenosine
Hydrogen ion + &alpha;-D-ribose-1-methylphosphonate-5-phosphate + S-Adenosylmethionine > &alpha;-D-ribose-1,2-cyclic-phosphate-5-phosphate + methane + 5'-Deoxyadenosine + L-Methionine
<i>S</i>-sulfanyl-[acceptor] + Dethiobiotin + S-Adenosylmethionine > an unsulfurated sulfur acceptor + Biotin + 5'-Deoxyadenosine + L-Methionine + Hydrogen ion
Coproporphyrinogen III + S-Adenosylmethionine > Protoporphyrinogen IX + Carbon dioxide + L-Methionine + 5'-Deoxyadenosine
5-Aminoimidazole ribonucleotide + S-Adenosylmethionine 4-Amino-2-methyl-5-phosphomethylpyrimidine + 5'-Deoxyadenosine + L-Methionine + Formic acid + carbon monoxide + Hydrogen ion
S-Adenosylmethionine + Ribonuc-tri-P-reductases-inactive <> 5'-Deoxyadenosine + L-Methionine + Ribonuc-tri-P-reductases-active
L-Tyrosine + S-Adenosylmethionine + a reduced electron acceptor > Dehydroglycine + p-Cresol + 5'-Deoxyadenosine + L-Methionine + an oxidized electron acceptor + Hydrogen ion
N-6-isopentyl adenosine-37 tRNA + S-Adenosylmethionine + <i>S</i>-sulfanyl-[acceptor] 2-methylthio-N-6-isopentyl adenosine-37 tRNA + S-Adenosylhomocysteine + L-Methionine + 5'-Deoxyadenosine + an unsulfurated sulfur acceptor + Hydrogen ion
6-Carboxy-5,6,7,8-tetrahydropterin + S-Adenosylmethionine + Hydrogen ion > 7-carboxy-7-deazaguanine + 5'-Deoxyadenosine + L-Methionine + Ammonia
2 S-Adenosylmethionine <> S-Adenosylhomocysteine +2 L-Methionine + 5'-Deoxyadenosine
2 S-Adenosylmethionine + Reduced acceptor <> S-Adenosylhomocysteine +2 L-Methionine + 5'-Deoxyadenosine
L-Tyrosine + S-Adenosylmethionine + NADPH <> 2-iminoacetate + p-Cresol + 5'-Deoxyadenosine + L-Methionine + NADP + Hydrogen ion
Dethiobiotin + 2 S-adenosyl-L-methionine + 2 Hydrogen ion + a sulfurated [sulfur carrier] > Biotin +2 L-Methionine +2 5'-Deoxyadenosine
Octanoyl-[acyl-carrier protein] + 2 a sulfur donor + 2 S-adenosyl-L-methionine > Lipoyl-ACP +2 L-Methionine + 5'-Deoxyadenosine
Protein N6-(octanoyl)lysine + 2 a sulfur donor + 2 S-adenosyl-L-methionine > Protein N6-(lipoyl)lysine +2 L-Methionine +2 5'-Deoxyadenosine
Protein N6-(octanoyl)lysine + 2 Reduced ferredoxin + 2 a sulfurated [sulfur carrier]? + 2 S-adenosyl-L-methionine >2 L-Methionine +2 5'-Deoxyadenosine + Oxidized ferredoxin + Protein N6-(lipoyl)lysine + an unsulfurated [sulfur carrier]
S-adenosyl-L-methionine + Coproporphyrinogen III > 5'-Deoxyadenosine + L-Methionine + Carbon dioxide + Protoporphyrinogen IX
L-Tyrosine + NADPH + S-adenosyl-L-methionine + L-Tyrosine + NADPH > Hydrogen ion + NADP + L-Methionine + 5'-Deoxyadenosine + p-Cresol + 2-iminoacetate
More...

Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-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
References
References:
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference: Lerner, Leon M. An improved preparation of 5'-deoxyadenosine by coupling methods. Carbohydrate Research (1988), 184 250-3.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID17319
HMDB IDHMDB01983
Pubchem Compound ID439182
Kegg IDC05198
ChemSpider ID388325
Wikipedia IDNot Available
BioCyc IDCH33ADO
EcoCyc IDCH33ADO
Ligand Expo5AD