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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:43:58 UTC

Update Date

2022-03-07 02:53:55 UTC

HMDB ID

HMDB0033958

Secondary Accession Numbers

HMDB33958

Metabolite Identification

Common Name

2-Deoxy-L-ribono-1,4-lactone

Description

2-Deoxy-L-ribono-1,4-lactone belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. 2-Deoxy-L-ribono-1,4-lactone has been detected, but not quantified in, herbs and spices. This could make 2-deoxy-L-ribono-1,4-lactone a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 2-Deoxy-L-ribono-1,4-lactone.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
4,5-dihydro-4-Hydroxy-5-(hydroxymethyl)-2(3H)-furanone	HMDB
L-erythro-Form	HMDB

Chemical Formula

C₅H₈O₄

Average Molecular Weight

132.1146

Monoisotopic Molecular Weight

132.042258744

IUPAC Name

4-hydroxy-5-(hydroxymethyl)oxolan-2-one

Traditional Name

4-hydroxy-5-(hydroxymethyl)oxolan-2-one

CAS Registry Number

38996-14-4

SMILES

OCC1OC(=O)CC1O

InChI Identifier

InChI=1S/C5H8O4/c6-2-4-3(7)1-5(8)9-4/h3-4,6-7H,1-2H2

InChI Key

YIXDEYPPAGPYDP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Gamma butyrolactones

Direct Parent

Gamma butyrolactones

Alternative Parents

Substituents

Gamma butyrolactone
Tetrahydrofuran
Secondary alcohol
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

a small molecule (DEOXYRIBONOLACTONE )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0033958)
Cytoplasm (HMDB: HMDB0033958)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033958)

Source

Exogenous

Exogenous (HMDB: HMDB0033958)

Food

Food (HMDB: HMDB0033958)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Plant

Plant (HMDB: HMDB0033958)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033958)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	972 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-1.4	ChemAxon
logS	0.87	ALOGPS
pKa (Strongest Acidic)	13.76	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	27.48 m³·mol⁻¹	ChemAxon
Polarizability	11.98 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]+	127.368	31661259
DarkChem	[M-H]-	121.919	31661259
DeepCCS	[M+H]+	128.452	30932474
DeepCCS	[M-H]-	126.296	30932474
DeepCCS	[M-2H]-	162.585	30932474
DeepCCS	[M+Na]+	137.253	30932474
AllCCS	[M+H]+	129.8	32859911
AllCCS	[M+H-H2O]+	125.2	32859911
AllCCS	[M+NH4]+	134.1	32859911
AllCCS	[M+Na]+	135.4	32859911
AllCCS	[M-H]-	123.3	32859911
AllCCS	[M+Na-2H]-	125.4	32859911
AllCCS	[M+HCOO]-	127.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Deoxy-L-ribono-1,4-lactone	OCC1OC(=O)CC1O	3090.2	Standard polar	33892256
2-Deoxy-L-ribono-1,4-lactone	OCC1OC(=O)CC1O	1246.7	Standard non polar	33892256
2-Deoxy-L-ribono-1,4-lactone	OCC1OC(=O)CC1O	1446.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Deoxy-L-ribono-1,4-lactone,1TMS,isomer #1	C[Si](C)(C)OCC1OC(=O)CC1O	1417.4	Semi standard non polar	33892256
2-Deoxy-L-ribono-1,4-lactone,1TMS,isomer #2	C[Si](C)(C)OC1CC(=O)OC1CO	1421.0	Semi standard non polar	33892256
2-Deoxy-L-ribono-1,4-lactone,2TMS,isomer #1	C[Si](C)(C)OCC1OC(=O)CC1O[Si](C)(C)C	1516.3	Semi standard non polar	33892256
2-Deoxy-L-ribono-1,4-lactone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(=O)CC1O	1671.7	Semi standard non polar	33892256
2-Deoxy-L-ribono-1,4-lactone,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC(=O)OC1CO	1674.3	Semi standard non polar	33892256
2-Deoxy-L-ribono-1,4-lactone,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(=O)CC1O[Si](C)(C)C(C)(C)C	1975.8	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9200000000-4e32049a4673a6de72bf	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone GC-MS (2 TMS) - 70eV, Positive	splash10-0fyc-9450000000-92d83ada9df91c9d60f9	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 10V, Positive-QTOF	splash10-001i-1900000000-37cb807f4f63e57d6ce5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 20V, Positive-QTOF	splash10-0159-3900000000-bbb62f307025d24b9a62	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 40V, Positive-QTOF	splash10-00xv-9000000000-38a36b53a7b96d4944b6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 10V, Negative-QTOF	splash10-001i-1900000000-0eb8bb3fc82b1aab62db	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 20V, Negative-QTOF	splash10-01qi-9700000000-d390b15a36bc9e01b6d3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 40V, Negative-QTOF	splash10-0006-9000000000-c8d05329baea64388483	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 10V, Negative-QTOF	splash10-01qc-9800000000-fb30290c6119bf8c65dc	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 20V, Negative-QTOF	splash10-000x-9300000000-b2e2864b1079ebb67689	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 40V, Negative-QTOF	splash10-0006-9000000000-f05d2843cb87988a637b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 10V, Positive-QTOF	splash10-015m-9700000000-e10ac42a02abedf43b83	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 20V, Positive-QTOF	splash10-006x-9100000000-bb8af714819eda1b9dd0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-L-ribono-1,4-lactone 40V, Positive-QTOF	splash10-0006-9000000000-6eeca0ca99324b4180c1	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB012177

KNApSAcK ID

C00054434

Chemspider ID

3826058

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

4635870

PDB ID

Not Available

ChEBI ID

173532

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 2-Deoxy-L-ribono-1,4-lactone (HMDB0033958)

MOL for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

3D MOL for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

3D SDF for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

3D-SDF for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

PDB for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

3D PDB for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

SMILES for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

INCHI for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

Structure for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

3D Structure for HMDB0033958 (2-Deoxy-L-ribono-1,4-lactone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra