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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-03-09 14:33:53 UTC

Update Date

2023-02-21 17:15:57 UTC

HMDB ID

HMDB0001900

Secondary Accession Numbers

HMDB01900

Metabolite Identification

Common Name

Ribonolactone

Description

Ribonolactone, 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
D-(+)-Ribonic acid gamma-lactone	ChEBI
D-Ribonic acid-1,4-lactone	ChEBI
D-Ribono-gamma-lactone	ChEBI
D-Ribonolactone	ChEBI
D-Ribopentono-1,4-lactone	ChEBI
Ribono-gamma-lactone	ChEBI
D-(+)-Ribonate g-lactone	Generator
D-(+)-Ribonate gamma-lactone	Generator
D-(+)-Ribonate γ-lactone	Generator
D-(+)-Ribonic acid g-lactone	Generator
D-(+)-Ribonic acid γ-lactone	Generator
D-Ribonate-1,4-lactone	Generator
D-Ribono-g-lactone	Generator
D-Ribono-γ-lactone	Generator
Ribono-g-lactone	Generator
Ribono-γ-lactone	Generator
D(+)-Ribonic acid gamma-lactone	HMDB
D-(+)-Ribonone-1.4-lactone	HMDB
D-ribono-1,4-Lactone	HMDB
delta-(+)-Ribonic acid g-lactone	HMDB
delta-(+)-Ribonic acid gamma-lactone	HMDB
delta-(+)-Ribonone-1.4-lactone	HMDB
delta-ribono-1,4-Lactone	HMDB
delta-ribono-gamma-Lactone	HMDB
delta-Ribonolactone	HMDB
delta-ribopentono-1,4-Lactone	HMDB
Deoxyribonolactone	HMDB
gamma-Lactone OF ribonate	HMDB
gamma-Lactone OF ribonic acid	HMDB
gamma-Lactone-ribonate	HMDB
gamma-Lactone-ribonic acid	HMDB
Ribonolactone	ChEBI

Chemical Formula

C₅H₈O₅

Average Molecular Weight

148.114

Monoisotopic Molecular Weight

148.037173366

IUPAC Name

(3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-one

Traditional Name

D-ribosone

CAS Registry Number

5336-08-3

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 Key

CUOKHACJLGPRHD-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

butan-4-olide (CHEBI:74168 )
ribonolactone (CHEBI:74168 )

Ontology

Physiological effect

Health effect

Nervous system disorder

Peripheral nervous system disorder

Neuroblastoma (HMDB: HMDB0001900)

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0001900)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0001900)

Source

Endogenous

Endogenous (HMDB: HMDB0001900)

Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)
Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)

Equine

Horse (FooDB: FOOD00378)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	83 - 85 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	1000000 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	847 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.1	ChemAxon
logS	0.76	ALOGPS
pKa (Strongest Acidic)	11.63	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	28.82 m³·mol⁻¹	ChemAxon
Polarizability	12.8 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	132.46	31661259
DarkChem	[M-H]-	125.546	31661259
AllCCS	[M+H]+	133.283	32859911
AllCCS	[M-H]-	123.925	32859911
DeepCCS	[M+H]+	132.459	30932474
DeepCCS	[M-H]-	130.256	30932474
DeepCCS	[M-2H]-	164.999	30932474
DeepCCS	[M+Na]+	139.4	30932474
AllCCS	[M+H]+	133.3	32859911
AllCCS	[M+H-H2O]+	128.8	32859911
AllCCS	[M+NH4]+	137.5	32859911
AllCCS	[M+Na]+	138.7	32859911
AllCCS	[M-H]-	123.9	32859911
AllCCS	[M+Na-2H]-	125.6	32859911
AllCCS	[M+HCOO]-	127.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Ribonolactone	OC[C@H]1OC(=O)[C@H](O)[C@@H]1O	2701.2	Standard polar	33892256
Ribonolactone	OC[C@H]1OC(=O)[C@H](O)[C@@H]1O	1635.4	Standard non polar	33892256
Ribonolactone	OC[C@H]1OC(=O)[C@H](O)[C@@H]1O	1432.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Ribonolactone,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(=O)[C@H](O)[C@@H]1O	1458.3	Semi standard non polar	33892256
Ribonolactone,1TMS,isomer #2	C[Si](C)(C)O[C@H]1C(=O)O[C@H](CO)[C@H]1O	1502.3	Semi standard non polar	33892256
Ribonolactone,1TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@@H](CO)OC(=O)[C@@H]1O	1492.5	Semi standard non polar	33892256
Ribonolactone,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O	1606.1	Semi standard non polar	33892256
Ribonolactone,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1OC(=O)[C@H](O)[C@@H]1O[Si](C)(C)C	1582.3	Semi standard non polar	33892256
Ribonolactone,2TMS,isomer #3	C[Si](C)(C)O[C@H]1C(=O)O[C@H](CO)[C@H]1O[Si](C)(C)C	1600.7	Semi standard non polar	33892256
Ribonolactone,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	1695.8	Semi standard non polar	33892256
Ribonolactone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(=O)[C@H](O)[C@@H]1O	1703.8	Semi standard non polar	33892256
Ribonolactone,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C(=O)O[C@H](CO)[C@H]1O	1742.8	Semi standard non polar	33892256
Ribonolactone,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)OC(=O)[C@@H]1O	1743.5	Semi standard non polar	33892256
Ribonolactone,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2052.0	Semi standard non polar	33892256
Ribonolactone,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1OC(=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2047.0	Semi standard non polar	33892256
Ribonolactone,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1C(=O)O[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C	2054.7	Semi standard non polar	33892256
Ribonolactone,3TBDMS,isomer #1	CC(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)C	2348.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Ribonolactone GC-MS (3 TMS)	splash10-0gb9-1940000000-94abb554de5192928a9d	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Ribonolactone GC-MS (Non-derivatized)	splash10-0gb9-1940000000-94abb554de5192928a9d	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Ribonolactone GC-EI-TOF (Non-derivatized)	splash10-0gba-0930000000-4632c741ce0480cf1b5a	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ribonolactone GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dl-9100000000-a5e444f62624dbfcd6fa	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ribonolactone GC-MS (3 TMS) - 70eV, Positive	splash10-0fmr-8495000000-9bc99dc8dea71b2b2868	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ribonolactone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ribonolactone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ribonolactone Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-001i-0900000000-c1cfbb14a5897b9ed6f8	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ribonolactone Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-0udi-2900000000-d5f9f85cfe0854052394	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Ribonolactone Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-004i-9100000000-d89f133906bd80602502	2012-07-24	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 10V, Positive-QTOF	splash10-000t-1900000000-b64ac3389c7d8b379f19	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 20V, Positive-QTOF	splash10-001j-1900000000-c09704319f6945661841	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 40V, Positive-QTOF	splash10-0007-9000000000-446348aa4d5976158197	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 10V, Negative-QTOF	splash10-0002-1900000000-791200554bb4c8c773e6	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 20V, Negative-QTOF	splash10-002b-1900000000-6ba9f7411098c2510897	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 40V, Negative-QTOF	splash10-052f-9000000000-60c2f7da80588ed50ba2	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 10V, Negative-QTOF	splash10-054k-8900000000-c714107d5f4ef369bf5f	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 20V, Negative-QTOF	splash10-0a4i-9200000000-bc8dd374ff0254696d9c	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 40V, Negative-QTOF	splash10-0006-9000000000-9a547cc1ba49997144c8	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 10V, Positive-QTOF	splash10-001i-2900000000-e907f82a388dab97e8a6	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 20V, Positive-QTOF	splash10-0mc3-9400000000-a5c59004054eb153ecbc	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ribonolactone 40V, Positive-QTOF	splash10-052f-9000000000-599e9990982d7f00bd09	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2012-12-04	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected and Quantified	21 (15 -86) umol/mmol creatinine	Children (1-13 years old)	Both	Neuroblastoma	699273	details

Associated Disorders and Diseases

Disease References

Neuroblastoma
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

256700 (Neuroblastoma)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022728

KNApSAcK ID

Not Available

Chemspider ID

99702

KEGG Compound ID

C02674

BioCyc ID

CPD-13413

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6380

PubChem Compound

111064

PDB ID

Not Available

ChEBI ID

74168

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1233571

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

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 ]
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 ]
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 ]

Showing metabocard for Ribonolactone (HMDB0001900)

MOL for HMDB0001900 (Ribonolactone)

3D MOL for HMDB0001900 (Ribonolactone)

3D SDF for HMDB0001900 (Ribonolactone)

3D-SDF for HMDB0001900 (Ribonolactone)

PDB for HMDB0001900 (Ribonolactone)

3D PDB for HMDB0001900 (Ribonolactone)

SMILES for HMDB0001900 (Ribonolactone)

INCHI for HMDB0001900 (Ribonolactone)

Structure for HMDB0001900 (Ribonolactone)

3D Structure for HMDB0001900 (Ribonolactone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra