beta-D-ribofuranose (PAMDB001172)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB001172
Identification
Name: beta-D-ribofuranose
Description:Beta-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
🔍MOLSDFPDBSMILESInChIView 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
Average Molecular Weight: 150.1299
Monoisotopic Molecular Weight: 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
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as monosaccharides. These 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.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassMonosaccharides
Direct Parent Monosaccharides
Alternative Parents
Substituents
  • Monosaccharide
  • Oxolane
  • Secondary alcohol
  • Polyol
  • Hemiacetal
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 95 °C
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility1070.0 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.96 m3·mol-1ChemAxon
Polarizability13.62 Å3ChemAxon
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
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
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
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 ID394477
Wikipedia IDNot Available
BioCyc IDCPD0-1108
EcoCyc IDCPD0-1108
Ligand ExpoHSU

Enzymes

Protein Details
• 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
Locus Tag:
PA4053
Molecular weight:
16.4 kDa
Reactions
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.

Transporters