D-Ribulose (ECMDB00621) (M2MDB000159)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)Transporters (1)XML
Proteins (95)
Record Information
Version2.0
Creation Date2012-05-31 10:27:55 -0600
Update Date2015-06-03 15:53:32 -0600
Secondary Accession Numbers
  • ECMDB00621
Identification
Name:D-Ribulose
DescriptionRibulose is a ketopentose - a monosaccharide containing five carbon atoms, and including a ketone functional group. D-ribulose is an intermediate in the fungal pathway for D-arabitol production. D-ribulose is the epimer of d-xylulose. (Wikipedia)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • D(-)-Ribulose
  • D-Adonose
  • D-Arabinulose
  • D-Araboketose
  • D-Erythro-2-Keptopentose
  • D-Erythro-Pentulose
  • D-Erythropentulose
  • D-Ribosone
  • D-Ribulose
  • Erythropentulose
Chemical Formula:C5H10O5
Weight:Average: 150.1299
Monoisotopic: 150.05282343
InChI Key:ZAQJHHRNXZUBTE-NQXXGFSBSA-N
InChI:InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5-/m1/s1
CAS number:488-84-6
IUPAC Name:(3R,4R)-1,3,4,5-tetrahydroxypentan-2-one
Traditional IUPAC Name:D-ribulose
SMILES:OC[C@@H](O)[C@@H](O)C(=O)CO
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
  • Beta-hydroxy ketone
  • Acyloin
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility678 g/LALOGPS
logP-2.2ALOGPS
logP-2.6ChemAxon
logS0.65ALOGPS
pKa (Strongest Acidic)10.57ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.6 m³·mol⁻¹ChemAxon
Polarizability13.47 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosine triphosphate + D-Ribulose <> ADP + D-Ribulose 5-phosphate
D-Ribulose + Adenosine triphosphate > Hydrogen ion + D-Ribulose-1-phosphate + ADP
D-arabinose <> D-Ribulose
Adenosine triphosphate + L-Ribulose + D-Ribulose <> ADP + L-Ribulose 5-phosphate + D-Ribulose 5-phosphate
D-Ribulose + Adenosine triphosphate + D-Ribulose > Adenosine diphosphate + Hydrogen ion + D-Ribulose-1-phosphate + ADP
D-Ribulose + Adenosine triphosphate > D-Ribulose-1-phosphate + Adenosine monophosphate + Hydrogen ion
D-arabinopyranose <> D-Ribulose
SMPDB Pathways:
D-arabinose degradation IPW002038 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 4 TMS)splash10-0lk9-2940000000-d972512c3992f5630d13View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0uyi-1920000000-4abe1c31075112542e5aView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0uyi-1920000000-cb182758b043e586b8d1View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0lk9-2940000000-d972512c3992f5630d13View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0uyi-1920000000-4abe1c31075112542e5aView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0uyi-1920000000-cb182758b043e586b8d1View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9000000000-5e0dfc74544a16cb6a2bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-00e9-9182200000-14fd007ef0237ffd6a29View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-000i-9200000000-afb0904788db599c35edView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-02t9-7900000000-10c3cccbf8dbb87ffeebView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0229-9800000000-a764f771911e773c02efView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-1900000000-9e2cd6df86b714a2a578View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9300000000-d2b653e8f893ae77c1e3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dm-9000000000-a0e9bde284b6cf02f608View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000j-9400000000-eff46a0627a1f3901e27View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06ri-9100000000-3ed3e568d42e85a3a856View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000000000-6e049d13c9659949bd3eView in MoNA
References
References:
  • Huck, J. H., Roos, B., Jakobs, C., van der Knaap, M. S., Verhoeven, N. M. (2004). "Evaluation of pentitol metabolism in mammalian tissues provides new insight into disorders of human sugar metabolism." Mol Genet Metab 82:231-237. Pubmed: 15234337
  • Ito M, Amano H, Yanagisawa I: Ribulose-peptide in human semen: II. Synthesis. Arch Androl. 1978;1(1):77-82. Pubmed: 570380
  • 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
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Drueckhammer, Dale G.; Durrwachter, J. Robert; Pederson, Richard L.; Crans, Debbie C.; Daniels, Lacy; Wong, Chi Huey. Reversible and in situ formation of organic arsenates and vanadates as organic phosphate mimics in enzymatic reactions: mechanistic inves
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID17173
HMDB IDHMDB00621
Pubchem Compound ID439203
Kegg IDC00309
ChemSpider ID133316
WikipediaD-Ribulose
BioCyc IDD-RIBULOSE
EcoCyc IDD-RIBULOSE

Enzymes

Protein Details
1. Ribulokinase
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + L(or D)-ribulose = ADP + L(or D)- ribulose 5-phosphate
Gene Name:
araB
Uniprot ID:
P08204
Molecular weight:
61089
Reactions
ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate.
Protein Details
2. L-fuculokinase
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + L-fuculose = ADP + L-fuculose 1- phosphate
Gene Name:
fucK
Uniprot ID:
P11553
Molecular weight:
53235
Reactions
ATP + L-fuculose = ADP + L-fuculose 1-phosphate.
Protein Details
3. L-fucose isomerase
General function:
Involved in L-fucose isomerase activity
Specific function:
Converts the aldose L-fucose into the corresponding ketose L-fuculose. Is also able to convert D-arabinose into D- ribulose, but this isomerase has a higher affinity for fucose and fuculose than for arabinose and ribulose, respectively
Gene Name:
fucI
Uniprot ID:
P69922
Molecular weight:
64976
Reactions
L-fucose = L-fuculose.

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