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Record Information
Version2.0
Creation Date2012-07-30 14:54:46 -0600
Update Date2015-06-03 17:20:48 -0600
Secondary Accession Numbers
  • ECMDB21175
Identification
Name:5'-Deoxyribose
Description5'-deoxyribose is a deoxy pentose meaning that it is derived from the sugar ribose by loss of an oxygen atom in the 5' position. The more common form of deoxyribose used in DNA is 2'deoxyribose. 5'-deoxyribose can be formed by the breakdown of 5'deoxyadenosine as catalyzed by 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.
Structure
Thumb
Synonyms:
  • (2R,3R,4R)-2,3,4-trihydroxypentanal
  • (2R,3R,4R)-2,3,4-trihydroxyvaleraldehyde
  • 5'-Deoxyribose
  • 5-Deoxy-aldehydo-D-ribose
  • 5-Deoxy-D-ribose
  • 5-Desoxy-D-ribose
  • D-Ribo-2,3,4-trihydroxyvaleraldehyde
Chemical Formula:C5H10O4
Weight:Average: 134.1305
Monoisotopic: 134.057908808
InChI Key:WDRISBUVHBMJEF-MROZADKFSA-N
InChI:InChI=1S/C5H10O4/c1-3(7)5(9)4(8)2-6/h2-5,7-9H,1H3/t3-,4+,5-/m1/s1
CAS number:Not Available
IUPAC Name:(2R,3R,4R)-2,3,4-trihydroxypentanal
Traditional IUPAC Name:5'-deoxyribose
SMILES:[H]O[C@@]([H])(C([H])=O)[C@]([H])(O[H])[C@]([H])(O[H])C([H])([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharides
Alternative Parents
Substituents
  • Monosaccharide
  • Beta-hydroxy aldehyde
  • Alpha-hydroxyaldehyde
  • Secondary alcohol
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Carbonyl group
  • Aldehyde
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility475 g/LALOGPS
logP-1.7ALOGPS
logP-1.9ChemAxon
logS0.55ALOGPS
pKa (Strongest Acidic)12.1ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity29.84 m³·mol⁻¹ChemAxon
Polarizability12.53 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kr-3900000000-30d57ef46048d7192e52View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-9200000000-ee1514b94bdabf4acfdeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9000000000-34bd0cb544ba73cb9e42View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-05ir-9400000000-41ed7612a81abf536ca6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-9200000000-ac0ef23d944837fa803aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9000000000-c450c0fcde2dbd7e339eView in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID62012
HMDB IDNot Available
Pubchem Compound ID45489773
Kegg IDNot Available
ChemSpider ID23346160
Wikipedia IDNot Available
BioCyc IDCPD0-2167
EcoCyc IDCPD0-2167

Enzymes

General function:
Involved in adenosylhomocysteine nucleosidase activity
Specific function:
Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. Can also use 5'-isobutylthioadenosine, 5'-n- butylthioadenosine, S-adenosyl-D-homocysteine, decarboxylated adenosylhomocysteine, deaminated adenosylhomocysteine and S-2-aza- adenosylhomocysteine as substrates
Gene Name:
mtnN
Uniprot ID:
P0AF12
Molecular weight:
24354
Reactions
S-adenosyl-L-homocysteine + H(2)O = S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine.
S-methyl-5'-thioadenosine + H(2)O = S-methyl-5-thio-D-ribose + adenine.

Transporters

General function:
Involved in transmembrane transport
Specific function:
Involved in the efflux of sugars. The physiological role may be the detoxification of non-metabolizable sugar analogs
Gene Name:
setC
Uniprot ID:
P31436
Molecular weight:
43493