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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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
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