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Showing metabocard for D-Ribulose (HMDB0000621)

IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-01-11 19:14:49 UTC
HMDB IDHMDB0000621
Secondary Accession Numbers
  • HMDB00621
Metabolite Identification
Common NameD-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. As the 1,5-bisphosphate, it combines with CO2 at the start of the photosynthetic process in green plants (carbon dioxide trap); d-ribulose is the epimer of d-xylulose. (Wikipedia).
Structure
Data?1547234089
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
D-ArabinoketoseChEBI
D-ArabinuloseChEBI
D-erythro-2-PentuloseChEBI
D-erythro-Pent-2-uloseChEBI
D-RiboketoseChEBI
D-RulChEBI
D(-)-RibuloseHMDB
D-AdonoseHMDB
D-AraboketoseHMDB
D-erythro-2-KeptopentoseHMDB
D-erythro-PentuloseHMDB
D-ErythropentuloseHMDB
D-RibosoneHMDB
Ribulose, (erythro-L)-isomerMeSH
DL-erythro-PentuloseMeSH
RibuloseMeSH
Ribulose, (erythro-D)-isomerMeSH
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name(3R,4R)-1,3,4,5-tetrahydroxypentan-2-one
Traditional NameD-ribulose
CAS Registry Number488-84-6
SMILES
OC[C@@H](O)[C@@H](O)C(=O)CO
InChI Identifier
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5-/m1/s1
InChI KeyZAQJHHRNXZUBTE-NQXXGFSBSA-N
Chemical Taxonomy
DescriptionThis compound 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
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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
Polarizability13.4 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
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
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Feces
Tissue Locations
  • Fibroblasts
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB004270
KNApSAcK IDC00001131
Chemspider ID133316
KEGG Compound IDC00309
BioCyc IDD-RIBULOSE
BiGG ID34569
Wikipedia LinkRibulose
METLIN ID5594
PubChem Compound151261
PDB IDNot Available
ChEBI ID17173
References
Synthesis ReferenceDrueckhammer, D.G.; Durrwachter, J.R.; Pederson, R.L.; Crans, D.C.; Wong, C.H. Reversible and in situ formation of organic arsenates and vanadates as organic phosphate mimics in enzymatic-reactions - mechanistic investigation of aldol reactions and synthetic applications. J.Org. Chem. 1989, 54, 70.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Huck JH, Roos B, Jakobs C, van der Knaap MS, Verhoeven NM: Evaluation of pentitol metabolism in mammalian tissues provides new insight into disorders of human sugar metabolism. Mol Genet Metab. 2004 Jul;82(3):231-7. [PubMed:15234337 ]
  2. Ito M, Amano H, Yanagisawa I: Ribulose-peptide in human semen: II. Synthesis. Arch Androl. 1978;1(1):77-82. [PubMed:570380 ]