Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-08-12 19:46:10 UTC
Update Date2022-09-22 18:34:17 UTC
HMDB IDHMDB0003371
Secondary Accession Numbers
  • HMDB03371
Metabolite Identification
Common NameL-Ribulose
DescriptionL-Ribulose, also known as β-L-ribulose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. L-Ribulose is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on L-Ribulose.
Structure
Data?1582752273
Synonyms
ValueSource
b-L-RibulofuranoseHMDB
Β-L-ribulofuranoseHMDB
L-Erythro-pentuloseHMDB
Β-L-erythro-2-pentulofuranoseHMDB
Β-L-ribuloseHMDB
beta-L-RibuloseHMDB
beta-L-Erythro-2-pentulofuranoseHMDB
L-RibuloseHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.13
Monoisotopic Molecular Weight150.052823422
IUPAC Name(2S,3S,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name(2S,3S,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry Number130271-85-1
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-/m0/s1
InChI KeyLQXVFWRQNMEDEE-YUPRTTJUSA-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
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Process
RoleNot Available
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 Solubility1310 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
Polarizability13.52 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]+131.96530932474
DeepCCS[M-H]-129.80530932474
DeepCCS[M-2H]-164.77530932474
DeepCCS[M+Na]+139.06930932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.10.73 minutes32390414
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.0.87 minutes32390414
Predicted by Siyang on May 30, 20229.9822 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.94 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid272.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid838.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid340.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid35.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid200.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid75.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid288.7 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid229.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)623.4 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid617.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid41.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid869.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid195.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid256.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate642.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA337.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water375.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

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

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
L-Ribulose,1TMS,isomer #1C[Si](C)(C)OC[C@]1(O)OC[C@H](O)[C@@H]1O1470.7Semi standard non polar33892256
L-Ribulose,1TMS,isomer #2C[Si](C)(C)O[C@@]1(CO)OC[C@H](O)[C@@H]1O1512.4Semi standard non polar33892256
L-Ribulose,1TMS,isomer #3C[Si](C)(C)O[C@H]1CO[C@@](O)(CO)[C@H]1O1488.0Semi standard non polar33892256
L-Ribulose,1TMS,isomer #4C[Si](C)(C)O[C@H]1[C@@H](O)CO[C@@]1(O)CO1491.9Semi standard non polar33892256
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-Ribulose,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@]1(O)OC[C@H](O)[C@@H]1O1695.6Semi standard non polar33892256
L-Ribulose,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@@]1(CO)OC[C@H](O)[C@@H]1O1739.3Semi standard non polar33892256
L-Ribulose,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1CO[C@@](O)(CO)[C@H]1O1683.0Semi standard non polar33892256
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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
L-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 - L-Ribulose GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - L-Ribulose 10V, Positive-QTOFsplash10-001i-2900000000-d014866a9eaa4bcc1c152021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - L-Ribulose 20V, Positive-QTOFsplash10-05fv-9000000000-fac868271cf0145b751c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - L-Ribulose 40V, Positive-QTOFsplash10-052e-9000000000-3310acb8673d3f763bfa2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - L-Ribulose 10V, Negative-QTOFsplash10-052b-8900000000-6174ea340f73118a4e712021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - L-Ribulose 20V, Negative-QTOFsplash10-056r-9000000000-3155b6a3b975db3bc6262021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - L-Ribulose 40V, Negative-QTOFsplash10-052f-9000000000-cc7ea805a3871cd388b52021-09-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023156
KNApSAcK IDC00019543
Chemspider ID8096058
KEGG Compound IDC00508
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkRibulose
METLIN IDNot Available
PubChem Compound9920423
PDB ID34V
ChEBI ID16880
Food Biomarker OntologyNot Available
VMH IDRBL_L
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceYasuda, Mari; Kawaguchi, Tomoko. Production method for L-ribulose from ribitol. Jpn. Kokai Tokkyo Koho (1999), 6 pp.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available