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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

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

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 Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
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.	1.22 minutes	32390414
Predicted by Siyang on May 30, 2022	10.1667 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.2 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	214.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	802.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	359.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	42.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	210.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	82.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	284.7 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	266.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	673.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	634.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	54.7 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	904.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	220.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	268.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	721.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	284.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	355.1 seconds	40023050

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

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 Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized