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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-03-07 02:49:04 UTC
HMDB IDHMDB0000621
Secondary Accession Numbers
  • HMDB00621
Metabolite Identification
Common NameD-Ribulose
DescriptionD-Ribulose (CAS: 488-84-6) is a ketopentose - a monosaccharide containing five carbon atoms, 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 ). Ribulose is also a microbial metabolite found in Acetobacter and Gluconobacter (PMID: 16232643 , 11272814 ).
Structure
Data?1582752144
Synonyms
ValueSource
D(-)-RibuloseHMDB
D-AdonoseHMDB
D-ArabinuloseHMDB
D-AraboketoseHMDB
D-ErythropentuloseHMDB
D-RibosoneHMDB
D-Erythro-2-ketopentoseHMDB
D-Erythro-pentuloseHMDB
beta-D-RibulofuranoseHMDB
beta-D-RibuloseHMDB
beta-D-Erythro-2-pentulofuranoseHMDB
Β-D-ribulofuranoseHMDB
Β-D-ribuloseHMDB
Β-D-erythro-2-pentulofuranoseHMDB
D-RibuloseHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.13
Monoisotopic Molecular Weight150.052823422
IUPAC Name(2R,3R,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name(2R,3R,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry Number131064-70-5
SMILES
OC[C@@]1(O)OC[C@@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4-,5-/m1/s1
InChI KeyLQXVFWRQNMEDEE-UOWFLXDJSA-N
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
  • Oxolane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location

Source

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility678 g/LALOGPS
logP-2.2ALOGPS
logP-2.1ChemAxon
logS0.94ALOGPS
pKa (Strongest Acidic)10.29ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.4 m³·mol⁻¹ChemAxon
Polarizability13.38 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+131.93330932474
DeepCCS[M-H]-129.7630932474
DeepCCS[M-2H]-164.54130932474
DeepCCS[M+Na]+138.6530932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
D-RibuloseOC[C@@]1(O)OC[C@@H](O)[C@H]1O3015.9Standard polar33892256
D-RibuloseOC[C@@]1(O)OC[C@@H](O)[C@H]1O1476.3Standard non polar33892256
D-RibuloseOC[C@@]1(O)OC[C@@H](O)[C@H]1O1431.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
D-Ribulose,1TMS,isomer #1C[Si](C)(C)OC[C@@]1(O)OC[C@@H](O)[C@H]1O1470.7Semi standard non polar33892256
D-Ribulose,1TMS,isomer #2C[Si](C)(C)O[C@]1(CO)OC[C@@H](O)[C@H]1O1512.4Semi standard non polar33892256
D-Ribulose,1TMS,isomer #3C[Si](C)(C)O[C@@H]1CO[C@](O)(CO)[C@@H]1O1488.0Semi standard non polar33892256
D-Ribulose,1TMS,isomer #4C[Si](C)(C)O[C@@H]1[C@H](O)CO[C@]1(O)CO1491.9Semi standard non polar33892256
D-Ribulose,2TMS,isomer #1C[Si](C)(C)OC[C@@]1(O[Si](C)(C)C)OC[C@@H](O)[C@H]1O1543.5Semi standard non polar33892256
D-Ribulose,2TMS,isomer #2C[Si](C)(C)OC[C@@]1(O)OC[C@@H](O[Si](C)(C)C)[C@H]1O1522.1Semi standard non polar33892256
D-Ribulose,2TMS,isomer #3C[Si](C)(C)OC[C@@]1(O)OC[C@@H](O)[C@H]1O[Si](C)(C)C1533.5Semi standard non polar33892256
D-Ribulose,2TMS,isomer #4C[Si](C)(C)O[C@@H]1CO[C@@](CO)(O[Si](C)(C)C)[C@@H]1O1550.1Semi standard non polar33892256
D-Ribulose,2TMS,isomer #5C[Si](C)(C)O[C@@H]1[C@H](O)CO[C@@]1(CO)O[Si](C)(C)C1551.0Semi standard non polar33892256
D-Ribulose,2TMS,isomer #6C[Si](C)(C)O[C@@H]1CO[C@](O)(CO)[C@@H]1O[Si](C)(C)C1523.5Semi standard non polar33892256
D-Ribulose,3TMS,isomer #1C[Si](C)(C)OC[C@@]1(O[Si](C)(C)C)OC[C@@H](O[Si](C)(C)C)[C@H]1O1594.3Semi standard non polar33892256
D-Ribulose,3TMS,isomer #2C[Si](C)(C)OC[C@@]1(O[Si](C)(C)C)OC[C@@H](O)[C@H]1O[Si](C)(C)C1591.6Semi standard non polar33892256
D-Ribulose,3TMS,isomer #3C[Si](C)(C)OC[C@@]1(O)OC[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C1569.2Semi standard non polar33892256
D-Ribulose,3TMS,isomer #4C[Si](C)(C)O[C@@H]1CO[C@@](CO)(O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1576.3Semi standard non polar33892256
D-Ribulose,4TMS,isomer #1C[Si](C)(C)OC[C@@]1(O[Si](C)(C)C)OC[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C1597.8Semi standard non polar33892256
D-Ribulose,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@]1(O)OC[C@@H](O)[C@H]1O1695.6Semi standard non polar33892256
D-Ribulose,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@]1(CO)OC[C@@H](O)[C@H]1O1739.3Semi standard non polar33892256
D-Ribulose,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@](O)(CO)[C@@H]1O1683.0Semi standard non polar33892256
D-Ribulose,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)CO[C@]1(O)CO1707.3Semi standard non polar33892256
D-Ribulose,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@]1(O[Si](C)(C)C(C)(C)C)OC[C@@H](O)[C@H]1O1978.8Semi standard non polar33892256
D-Ribulose,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@]1(O)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O1957.4Semi standard non polar33892256
D-Ribulose,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@]1(O)OC[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C1980.1Semi standard non polar33892256
D-Ribulose,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@@](CO)(O[Si](C)(C)C(C)(C)C)[C@@H]1O2000.0Semi standard non polar33892256
D-Ribulose,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)CO[C@@]1(CO)O[Si](C)(C)C(C)(C)C2002.1Semi standard non polar33892256
D-Ribulose,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@](O)(CO)[C@@H]1O[Si](C)(C)C(C)(C)C1966.2Semi standard non polar33892256
D-Ribulose,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@]1(O[Si](C)(C)C(C)(C)C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O2278.8Semi standard non polar33892256
D-Ribulose,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@]1(O[Si](C)(C)C(C)(C)C)OC[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C2266.1Semi standard non polar33892256
D-Ribulose,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@]1(O)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C2267.0Semi standard non polar33892256
D-Ribulose,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@@](CO)(O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2275.9Semi standard non polar33892256
D-Ribulose,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@]1(O[Si](C)(C)C(C)(C)C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C2519.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_3_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_3_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_3_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TMS_4_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_1_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_2_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Ribulose GC-MS (TBDMS_2_5) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ribulose 10V, Negative-QTOFsplash10-052b-8900000000-6174ea340f73118a4e712021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ribulose 20V, Negative-QTOFsplash10-056r-9000000000-3155b6a3b975db3bc6262021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ribulose 40V, Negative-QTOFsplash10-052f-9000000000-cc7ea805a3871cd388b52021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ribulose 10V, Positive-QTOFsplash10-001i-2900000000-d014866a9eaa4bcc1c152021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ribulose 20V, Positive-QTOFsplash10-05fv-9000000000-fac868271cf0145b751c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Ribulose 40V, Positive-QTOFsplash10-052e-9000000000-3310acb8673d3f763bfa2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Feces
Tissue Locations
  • Fibroblasts
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>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
FooDB IDFDB004270
KNApSAcK IDC00001131
Chemspider ID10254592
KEGG Compound IDC00309
BioCyc IDD-RIBULOSE
BiGG IDNot Available
Wikipedia LinkRibulose
METLIN IDNot Available
PubChem Compound12358756
PDB IDNot Available
ChEBI ID17173
Food Biomarker OntologyNot Available
VMH IDRBL_D
MarkerDB IDNot Available
Good Scents IDNot Available
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 ]
  3. Ahmed Z, Shimonishi T, Bhuiyan SH, Utamura M, Takada G, Izumori K: Biochemical preparation of L-ribose and L-arabinose from ribitol: a new approach. J Biosci Bioeng. 1999;88(4):444-8. [PubMed:16232643 ]
  4. Adachi O, Fujii Y, Ano Y, Moonmangmee D, Toyama H, Shinagawa E, Theeragool G, Lotong N, Matsushita K: Membrane-bound sugar alcohol dehydrogenase in acetic acid bacteria catalyzes L-ribulose formation and NAD-dependent ribitol dehydrogenase is independent of the oxidative fermentation. Biosci Biotechnol Biochem. 2001 Jan;65(1):115-25. doi: 10.1271/bbb.65.115. [PubMed:11272814 ]
  5. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]