Showing metabocard for 5'-Deoxyadenosine (BMDB0001983)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
Record Information
Version1.0
Creation Date2016-09-30 22:49:33 UTC
Update Date2020-04-22 15:09:16 UTC
BMDB IDBMDB0001983
Secondary Accession Numbers
  • BMDB01983
Metabolite Identification
Common Name5'-Deoxyadenosine
Description5'-Deoxyadenosine 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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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 exists in all living species, ranging from bacteria to plants to humans. Based on a literature review a significant number of articles have been published on 5'-Deoxyadenosine.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
5'-Deoxy-adenosineHMDB
5'-DAdo nucleosideMeSH, HMDB
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
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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Mitochondria
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
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
BioavailabilityYesChemAxon
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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-7753a248c8f9e8bd3c17View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000i-0910000000-89ee982504aa7d7e8d86View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-000i-0900000000-88f38e28bec54de698ebView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-00kr-2900000000-7f30e8fa287a8c04426fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000i-0900000000-0b1ad0521a9e5b4f4e69View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-33ce25ce3b126b922477View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-5ffeb1c5e0b4ba70a9a0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-000i-0900000000-94d5e457c8b194127db1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-001i-0910000000-5ef9ec3078fd4597497fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-000i-0910000000-896c15b06d2fe2a894beView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-001i-0900000000-0364ac4f65cbde9247abView 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
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001983
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022781
KNApSAcK IDNot Available
Chemspider ID388325
KEGG Compound IDC05198
BioCyc IDCH33ADO
BiGG ID45324
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439182
PDB IDNot Available
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)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Lipoyl synthase, mitochondrial
General function:
Coenzyme transport and metabolism
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.
Gene Name:
LIAS
Uniprot ID:
Q5BIP7
Molecular weight:
42035.0