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2'-Deoxyadenosine (YMDB00503)

Identification
YMDB IDYMDB00503
Name2'-Deoxyadenosine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDeoxyadenosine, also known as dA, belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2. Deoxyadenosine is a strong basic compound (based on its pKa). Deoxyadenosine exists in all living species, ranging from bacteria to humans. Deoxyadenosine is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)tetrahydrofuran-3-ol
  • 2-Deoxyadenosine
  • 2-deoxyadenosine 5-triphosphate
  • 2'-Deoxy-5'-ATP
  • 2'-Deoxy-ATP
  • 2'-Deoxyadenosine
  • 2'-Deoxyadenosine 5'-triphosphate
  • 2'-deoxyadenosine triphosphate
  • 5-(6-AMINO-PURIN-9-YL)-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-OL
  • 9-(2-Deoxy-beta-D-erythro-pentofuranosyl)adenine
  • 9-(2-deoxy-beta-D-ribofuranosyl)-9H-purin-6-amine
  • 9H-Purin-6-amine, 9-(2-deoxy-beta-D-ribofuranosyl)-
  • Adenine deoxy nucleoside
  • Adenine deoxyribonucleoside
  • Adenosine, 2'-deoxy-
  • Adenyldeoxyriboside
  • beta-D-Erythro-Pentofuranoside, adenine-9 2-deoxy-
  • beta-D-Ribofuranose, 1-(6-amino-9H-purin-9-yl)-1,2-dideoxy-
  • dA
  • dATP
  • Deoxy-ATP
  • Deoxyadenosine
  • deoxyadenosine 5-triphosphate
  • Deoxyadenosine 5'-triphosphate
  • deoxyadenosine triphosphate
  • deoxyadenosine-triphosphate
  • Desoxyadenosine
  • DTP
  • 9-(2-Deoxy-b-D-erythro-pentofuranosyl)adenine
  • 9-(2-Deoxy-β-D-erythro-pentofuranosyl)adenine
  • 9-(2-Deoxy-b-D-ribofuranosyl)-9H-purin-6-amine
  • 9-(2-Deoxy-β-D-ribofuranosyl)-9H-purin-6-amine
  • 1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-b-D-ribofuranose
  • 1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-beta-D-ribofuranose
  • 1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-beta-delta-ribofuranose
  • 9-(2-Deoxy-b-D-erythro-pentofuranosyl)-9H-purin-6-amine
  • 9-(2-Deoxy-beta-D-erythro-pentofuranosyl)-9H-purin-6-amine
  • 9-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-9H-purin-6-amine
  • 9-(2-Deoxy-beta-delta-erythro-pentofuranosyl)adenine
  • 9-(2-Deoxy-beta-delta-ribofuranosyl)-9H-purin-6-amine
  • Adenine deoxyribose
  • Adenine-9 2-deoxy-b-D-erythro-pentofuranoside
  • Adenine-9 2-deoxy-beta-D-erythro-pentofuranoside
  • Adenine-9 2-deoxy-beta-delta-erythro-pentofuranoside
CAS numberNot Available
WeightAverage: 251.2419
Monoisotopic: 251.101839307
InChI KeyOLXZPDWKRNYJJZ-RRKCRQDMSA-N
InChIInChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1
IUPAC Name(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol
Traditional IUPAC Name2-deoxyadenosine
Chemical FormulaC10H13N5O3
SMILESNC1=C2N=CN([C@H]3C[C@H](O)[C@@H](CO)O3)C2=NC=N1
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleosides
Sub ClassPurine 2'-deoxyribonucleosides
Direct ParentPurine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside
  • 6-aminopurine
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • N-substituted imidazole
  • Pyrimidine
  • Imidolactam
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Amine
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Alcohol
  • Organic nitrogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP-0.55 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility10.7 g/LALOGPS
logP-0.95ALOGPS
logP-1.2ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)13.89ChemAxon
pKa (Strongest Basic)3.94ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area119.31 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity61.68 m³·mol⁻¹ChemAxon
Polarizability24.24 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Lipoic acid metabolismPW002499 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesisPW002478 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Lipoic acid metabolismec00785 Map00785
Purine metabolismec00230 Map00230
SMPDB Reactions
Octanoyl-[acyl-carrier protein] + S-Adenosyl-L-methionine + a sulfur donor → Lipoyl-ACP + L-Methionine + 2'-Deoxyadenosine
a sulfur donor + Protein N6-(octanoyl)lysine + S-Adenosyl-L-methionine → L-Methionine + Protein N6-(lipoyl)lysine + 2'-Deoxyadenosine
KEGG Reactions
dAMP + water → phosphate + 2'-Deoxyadenosine
water + hydron + 2'-Deoxyadenosine → 2'-Deoxyinosine + Ammonium
phosphate + 2'-Deoxyadenosine ↔ 2-deoxy-D-ribofuranose 1-phosphate + Adenine
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-0pbc-1950000000-892b755b10f34bcfa1c7JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)splash10-05fr-9750000000-34ebf7e59598c6551f52JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0pbc-2950000000-9d52e7dcd83de5a30aefJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0pbc-1950000000-892b755b10f34bcfa1c7JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-05fr-9750000000-34ebf7e59598c6551f52JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0pbc-2950000000-9d52e7dcd83de5a30aefJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-000x-9550000000-219c39ab05ecbebb53eeJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0ge9-6917000000-51808985bdc9abeb3cb3JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-0udr-1790000000-c0d4c0cc085cab7c2dcfJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-000i-1900000000-e2abd19062db64ff67beJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-000i-2900000000-1b8d5c847c2b1955056eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-000i-5900000000-845c20e0f6bd5494b6dcJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-004r-8900000000-484d9f08e4e28fab1f70JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-000i-0900000000-e852451e7253e0de72beJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-0udi-0390000000-fba17d1430b371138db2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-000i-0930000000-931c7b084c33f9122af4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-001i-0900000000-66ae7ac8bd510a173402JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-001i-0900000000-c71d67857e2136dc7666JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0udr-1790000000-cfbdf2e3950e7987b94bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-1900000000-a3c367588a28d36cf5f0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-2900000000-1b8d5c847c2b1955056eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-5900000000-f950493ce420caae6a66JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004r-8900000000-61ed5b4b3e748a449803JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-000i-0900000000-31d03c242f14d91a718cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0udi-0390000000-fba17d1430b371138db2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-000i-0930000000-931c7b084c33f9122af4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-000i-0900000000-81ac782a59b2ca52f52bJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0920000000-2e897a458cf4c7af381cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-f52b5322fde2e3722903JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-fcb0a5032b8607fd8b11JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0290000000-bec96a9658c683fa0d9bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-0910000000-b504aa725d20d6213b20JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-053r-2900000000-d09551db93d558a5aed7JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., Rabinowitz, J. D. (2010). "Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations." Mol Biol Cell 21:198-211.19889834
Synthesis Reference:Munch-Petersen, Agnete. Formation in vitro of deoxyadenosine triphosphate from deoxyadenosine in Ehrlich ascites cells. Biochemical and Biophysical Research Communications (1960), 3 392-6.
External Links:
ResourceLink
CHEBI ID17256
HMDB IDHMDB00101
Pubchem Compound ID22209663
Kegg IDC00131
ChemSpider ID24765642
FOODB IDFDB021894
WikipediaDeoxyadenosine
BioCyc IDDEOXYADENOSINE

Enzymes

Protein Details
1. Purine nucleoside phosphorylase
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:
PNP1
Uniprot ID:
Q05788
Molecular weight:
33754.60156
Reactions
Purine nucleoside + phosphate → purine + alpha-D-ribose 1-phosphate.
Protein Details
2. Adenosine deaminase
General function:
Involved in deaminase activity
Specific function:
Adenosine + H(2)O = inosine + NH(3)
Gene Name:
AAH1
Uniprot ID:
P53909
Molecular weight:
39634.69922
Reactions
Adenosine + H(2)O → inosine + NH(3).
Protein Details
3. Lipoyl synthase, mitochondrial
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.