Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-03-09 14:33:53 UTC
Update Date2021-10-13 04:36:19 UTC
HMDB IDHMDB0001900
Secondary Accession Numbers
  • HMDB01900
Metabolite Identification
Common NameRibonolactone
DescriptionRibonolactone, also known as D-ribono-1,4-lactone is a five-membered form of ribonolactone having D-configuration. It has a role as a metabolite. It is a ribonolactone and a butan-4-olide. It derives from a D-ribonic acid. Ribonolactone belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Ribonolactone is a metabolite normally not detectable in human biofluids; however, it has been found in the urine of patients with neuroblastoma.
Structure
Data?1582752215
Synonyms
ValueSource
D-(+)-Ribonic acid gamma-lactoneChEBI
D-Ribonic acid-1,4-lactoneChEBI
D-Ribono-gamma-lactoneChEBI
D-RibonolactoneChEBI
D-Ribopentono-1,4-lactoneChEBI
Ribono-gamma-lactoneChEBI
D-(+)-Ribonate g-lactoneGenerator
D-(+)-Ribonate gamma-lactoneGenerator
D-(+)-Ribonate γ-lactoneGenerator
D-(+)-Ribonic acid g-lactoneGenerator
D-(+)-Ribonic acid γ-lactoneGenerator
D-Ribonate-1,4-lactoneGenerator
D-Ribono-g-lactoneGenerator
D-Ribono-γ-lactoneGenerator
Ribono-g-lactoneGenerator
Ribono-γ-lactoneGenerator
D(+)-Ribonic acid gamma-lactoneHMDB
D-(+)-Ribonone-1.4-lactoneHMDB
D-ribono-1,4-LactoneHMDB
delta-(+)-Ribonic acid g-lactoneHMDB
delta-(+)-Ribonic acid gamma-lactoneHMDB
delta-(+)-Ribonone-1.4-lactoneHMDB
delta-ribono-1,4-LactoneHMDB
delta-ribono-gamma-LactoneHMDB
delta-RibonolactoneHMDB
delta-ribopentono-1,4-LactoneHMDB
DeoxyribonolactoneHMDB
gamma-Lactone OF ribonateHMDB
gamma-Lactone OF ribonic acidHMDB
gamma-Lactone-ribonateHMDB
gamma-Lactone-ribonic acidHMDB
RibonolactoneChEBI
Chemical FormulaC5H8O5
Average Molecular Weight148.114
Monoisotopic Molecular Weight148.037173366
IUPAC Name(3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-one
Traditional NameD-ribosone
CAS Registry Number5336-08-3
SMILES
OC[C@H]1OC(=O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H8O5/c6-1-2-3(7)4(8)5(9)10-2/h2-4,6-8H,1H2/t2-,3-,4-/m1/s1
InChI KeyCUOKHACJLGPRHD-BXXZVTAOSA-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
  • Gamma butyrolactone
  • Tetrahydrofuran
  • Carboxylic acid ester
  • Lactone
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Primary alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point83 - 85 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility847 g/LALOGPS
logP10(-2) g/LALOGPS
logP10(-2.1) g/LChemAxon
logS10(0.76) g/LALOGPS
pKa (Strongest Acidic)11.63ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.99 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.82 m³·mol⁻¹ChemAxon
Polarizability12.8 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
DarkChem[M+H]+132.4631661259
DarkChem[M-H]-125.54631661259
AllCCS[M+H]+133.28332859911
AllCCS[M-H]-123.92532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
RibonolactoneOC[C@H]1OC(=O)[C@H](O)[C@@H]1O2701.2Standard polar33892256
RibonolactoneOC[C@H]1OC(=O)[C@H](O)[C@@H]1O1635.4Standard non polar33892256
RibonolactoneOC[C@H]1OC(=O)[C@H](O)[C@@H]1O1432.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Ribonolactone,1TMS,isomer #1C[Si](C)(C)OC[C@H]1OC(=O)[C@H](O)[C@@H]1O1458.3Semi standard non polar33892256
Ribonolactone,1TMS,isomer #2C[Si](C)(C)O[C@H]1C(=O)O[C@H](CO)[C@H]1O1502.3Semi standard non polar33892256
Ribonolactone,1TMS,isomer #3C[Si](C)(C)O[C@@H]1[C@@H](CO)OC(=O)[C@@H]1O1492.5Semi standard non polar33892256
Ribonolactone,2TMS,isomer #1C[Si](C)(C)OC[C@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O1606.1Semi standard non polar33892256
Ribonolactone,2TMS,isomer #2C[Si](C)(C)OC[C@H]1OC(=O)[C@H](O)[C@@H]1O[Si](C)(C)C1582.3Semi standard non polar33892256
Ribonolactone,2TMS,isomer #3C[Si](C)(C)O[C@H]1C(=O)O[C@H](CO)[C@H]1O[Si](C)(C)C1600.7Semi standard non polar33892256
Ribonolactone,3TMS,isomer #1C[Si](C)(C)OC[C@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1695.8Semi standard non polar33892256
Ribonolactone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1OC(=O)[C@H](O)[C@@H]1O1703.8Semi standard non polar33892256
Ribonolactone,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C(=O)O[C@H](CO)[C@H]1O1742.8Semi standard non polar33892256
Ribonolactone,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)OC(=O)[C@@H]1O1743.5Semi standard non polar33892256
Ribonolactone,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1OC(=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2052.0Semi standard non polar33892256
Ribonolactone,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@H]1OC(=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2047.0Semi standard non polar33892256
Ribonolactone,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1C(=O)O[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C2054.7Semi standard non polar33892256
Ribonolactone,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1OC(=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2348.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Ribonolactone GC-MS (3 TMS)splash10-0gb9-1940000000-94abb554de5192928a9d2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Ribonolactone GC-MS (Non-derivatized)splash10-0gb9-1940000000-94abb554de5192928a9d2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Ribonolactone GC-EI-TOF (Non-derivatized)splash10-0gba-0930000000-4632c741ce0480cf1b5a2017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribonolactone GC-MS (Non-derivatized) - 70eV, Positivesplash10-00dl-9100000000-a5e444f62624dbfcd6fa2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribonolactone GC-MS (3 TMS) - 70eV, Positivesplash10-0fmr-8495000000-9bc99dc8dea71b2b28682017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribonolactone GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ribonolactone GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribonolactone Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-001i-0900000000-c1cfbb14a5897b9ed6f82012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribonolactone Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-0udi-2900000000-d5f9f85cfe08540523942012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ribonolactone Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-004i-9100000000-d89f133906bd806025022012-07-24HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 10V, Positive-QTOFsplash10-000t-1900000000-b64ac3389c7d8b379f192017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 20V, Positive-QTOFsplash10-001j-1900000000-c09704319f69456618412017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 40V, Positive-QTOFsplash10-0007-9000000000-446348aa4d59761581972017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 10V, Negative-QTOFsplash10-0002-1900000000-791200554bb4c8c773e62017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 20V, Negative-QTOFsplash10-002b-1900000000-6ba9f7411098c25108972017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 40V, Negative-QTOFsplash10-052f-9000000000-60c2f7da80588ed50ba22017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 10V, Negative-QTOFsplash10-054k-8900000000-c714107d5f4ef369bf5f2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 20V, Negative-QTOFsplash10-0a4i-9200000000-bc8dd374ff0254696d9c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 40V, Negative-QTOFsplash10-0006-9000000000-9a547cc1ba49997144c82021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 10V, Positive-QTOFsplash10-001i-2900000000-e907f82a388dab97e8a62021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 20V, Positive-QTOFsplash10-0mc3-9400000000-a5c59004054eb153ecbc2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ribonolactone 40V, Positive-QTOFsplash10-052f-9000000000-599e9990982d7f00bd092021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified21 (15 -86) umol/mmol creatinineChildren (1-13 years old)BothNeuroblastoma details
Associated Disorders and Diseases
Disease References
Neuroblastoma
  1. Gates SC, Sweeley CC, Krivit W, DeWitt D, Blaisdell BE: Automated metabolic profiling of organic acids in human urine. II. Analysis of urine samples from "healthy" adults, sick children, and children with neuroblastoma. Clin Chem. 1978 Oct;24(10):1680-9. [PubMed:699273 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022728
KNApSAcK IDNot Available
Chemspider ID99702
KEGG Compound IDC02674
BioCyc IDCPD-13413
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6380
PubChem Compound111064
PDB IDNot Available
ChEBI ID74168
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1233571
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Lewis S, Kenyon CN, Meili J, Burlingame AL: High resolution gas chromatographic/real-time high resolution mass spectrometric identification of organic acids in human urine. Anal Chem. 1979 Jul;51(8):1275-85. [PubMed:484857 ]
  2. Chamberlin BA, Sweeley CC: Metabolic profiles of urinary organic acids recovered from absorbent filter paper. Clin Chem. 1987 Apr;33(4):572-6. [PubMed:3829393 ]
  3. Gates SC, Sweeley CC, Krivit W, DeWitt D, Blaisdell BE: Automated metabolic profiling of organic acids in human urine. II. Analysis of urine samples from "healthy" adults, sick children, and children with neuroblastoma. Clin Chem. 1978 Oct;24(10):1680-9. [PubMed:699273 ]