beta-D-ribofuranose (ECMDB20343) (M2MDB001172)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)Transporters (1)XML
Proteins (86)
Record Information
Version2.0
Creation Date2012-05-31 14:40:04 -0600
Update Date2015-07-07 11:22:39 -0600
Secondary Accession Numbers
  • ECMDB20343
Identification
Name:beta-D-ribofuranose
DescriptionBeta-D-ribofuranose is the cyclic form of D-ribose. Ribose, primarily occurring as D-ribose, is an organic compound that occurs widely in nature. It is an aldopentose, a monosaccharide containing five carbon atoms that in its acyclic form has an aldehyde functional group at one end. Typically, ribose exists in the cyclic form. It comprises the backbone of RNA, a biopolymer that is the basis of genetic transcription. It is related to deoxyribose, as found in DNA, by the removal of one hydroxy group. Once phosphorylated, ribose can become a subunit of ATP, NADH, and several other compounds that are critical to metabolism.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms:
  • a D-Ribose
  • a-D-Ribofuranose
  • a-D-Ribose
  • a-D-Ribose-5
  • a-delta-Ribose
  • a-delta-Ribose-5
  • a-δ-Ribose
  • a-δ-Ribose-5
  • Alpha D-Ribose
  • Alpha-D-Ribofuranose
  • Alpha-D-Ribose
  • Alpha-D-Ribose-5
  • Alpha-delta-Ribose
  • Alpha-delta-Ribose-5
  • b-D-Rib
  • b-D-Ribofuranose
  • b-D-Ribofuranosyl
  • b-D-Ribopyranose
  • b-D-Ribose
  • BDR
  • Beta-D-Rib
  • Beta-D-Ribofuranose
  • Beta-D-Ribofuranosyl
  • Beta-D-Ribopyranose
  • Beta-D-Ribose
  • D-(-)-Ribose
  • D-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  • D-Ribose
  • Delta-(-)-Ribose
  • Delta-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  • Delta-Ribose
  • Pentose
  • RIB
  • Ribose
  • α D-Ribose
  • α-D-Ribofuranose
  • α-D-Ribose
  • α-D-Ribose-5
  • α-δ-Ribose
  • α-δ-Ribose-5
  • β-D-Rib
  • β-D-Ribofuranose
  • β-D-Ribofuranosyl
  • β-D-Ribopyranose
  • β-D-Ribose
  • δ-(-)-Ribose
  • δ-ribo-2,3,4,5-Tetrahydroxyvaleraldehyde
  • δ-Ribose
Chemical Formula:C5H10O5
Weight:Average: 150.1299
Monoisotopic: 150.05282343
InChI Key:HMFHBZSHGGEWLO-TXICZTDVSA-N
InChI:InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5-/m1/s1
CAS number:50-69-1
IUPAC Name:(2R,3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional IUPAC Name:β-D-ribofuranoside
SMILES:[H][C@@]1(O)O[C@]([H])(CO)[C@@]([H])(O)[C@@]1([H])O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:0
Melting point:95 °C
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility1070 g/LALOGPS
logP-2.6ALOGPS
logP-2.3ChemAxon
logS0.85ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.62 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
beta-D-Ribopyranose <> beta-D-ribofuranose
beta-D-ribofuranose <> D-ribose
beta-D-ribofuranose <> beta-D-Ribopyranose
beta-D-Ribopyranose > beta-D-ribofuranose
Adenosine + Water > beta-D-ribofuranose + Adenine
SMPDB Pathways:
Ribose DegradationPW002102 ThumbThumb?image type=greyscaleThumb?image type=simple
adenine and adenosine salvage IIIPW002072 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0ue9-2900000000-8fa37f7dc67540d4891dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f89-2900000000-3aa93cae85372f29343aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052e-9100000000-1a435a9ab54e07c29342View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-1900000000-a448ec0037ce8a3e1ca9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001j-2900000000-a743b6fdefffedf3c07cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-812bdd2c7abfbde5360eView 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:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID47002
HMDB IDNot Available
Pubchem Compound ID447347
Kegg IDC16639
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD0-1108
EcoCyc IDCPD0-1108
Ligand ExpoHSU

Enzymes

Protein Details
1. Riboflavin synthase alpha chain
General function:
Involved in riboflavin synthase activity
Specific function:
Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)- ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2- butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The alpha subunit catalyzes the dismutation of 6,7-dimethyl-8-lumazine to riboflavin and 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)- pyrimidinedione
Gene Name:
ribE
Uniprot ID:
P0AFU8
Molecular weight:
23445
Reactions
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.
Protein Details
2. D-ribose pyranase
General function:
Involved in intramolecular lyase activity
Specific function:
Catalyzes the interconversion of beta-pyran and beta- furan forms of D-ribose. It also catalyzes the conversion between beta-allofuranose and beta-allopyranose
Gene Name:
rbsD
Uniprot ID:
P04982
Molecular weight:
15292
Reactions
Beta-D-ribopyranose = beta-D-ribofuranose.
Beta-D-allopyranose = beta-D-allofuranose.

Transporters

Protein Details
1. Sugar efflux transporter C
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