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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:41:37 UTC

Update Date

2022-03-07 02:53:54 UTC

HMDB ID

HMDB0033919

Secondary Accession Numbers

HMDB33919

Metabolite Identification

Common Name

2-Deoxy-D-ribitol

Description

2-Deoxy-D-ribitol belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl). 2-Deoxy-D-ribitol has been detected, but not quantified in, herbs and spices. This could make 2-deoxy-D-ribitol a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 2-Deoxy-D-ribitol.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₅H₁₂O₄

Average Molecular Weight

136.1464

Monoisotopic Molecular Weight

136.073558872

IUPAC Name

pentane-1,2,3,5-tetrol

Traditional Name

pentane-1,2,3,5-tetrol

CAS Registry Number

Not Available

SMILES

OCCC(O)C(O)CO

InChI Identifier

InChI=1S/C5H12O4/c6-2-1-4(8)5(9)3-7/h4-9H,1-3H2

InChI Key

ZDAWZDFBPUUDAY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Secondary alcohols

Alternative Parents

Substituents

Secondary alcohol
Polyol
Hydrocarbon derivative
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0033919)
Cytoplasm (HMDB: HMDB0033919)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033919)

Source

Exogenous

Exogenous (HMDB: HMDB0033919)

Food

Food (HMDB: HMDB0033919)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Plant

Plant (HMDB: HMDB0033919)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033919)

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	669 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.4	ChemAxon
logS	0.69	ALOGPS
pKa (Strongest Acidic)	13.32	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	31.34 m³·mol⁻¹	ChemAxon
Polarizability	13.57 Å³	ChemAxon
Number of Rings	0	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]+	128.754	31661259
DarkChem	[M-H]-	122.723	31661259
DeepCCS	[M+H]+	128.049	30932474
DeepCCS	[M-H]-	125.333	30932474
DeepCCS	[M-2H]-	161.873	30932474
DeepCCS	[M+Na]+	136.535	30932474
AllCCS	[M+H]+	132.6	32859911
AllCCS	[M+H-H2O]+	128.5	32859911
AllCCS	[M+NH4]+	136.4	32859911
AllCCS	[M+Na]+	137.5	32859911
AllCCS	[M-H]-	126.0	32859911
AllCCS	[M+Na-2H]-	128.6	32859911
AllCCS	[M+HCOO]-	131.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Deoxy-D-ribitol	OCCC(O)C(O)CO	2788.6	Standard polar	33892256
2-Deoxy-D-ribitol	OCCC(O)C(O)CO	1452.1	Standard non polar	33892256
2-Deoxy-D-ribitol	OCCC(O)C(O)CO	1411.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Deoxy-D-ribitol,1TMS,isomer #1	C[Si](C)(C)OCCC(O)C(O)CO	1445.3	Semi standard non polar	33892256
2-Deoxy-D-ribitol,1TMS,isomer #2	C[Si](C)(C)OC(CCO)C(O)CO	1428.5	Semi standard non polar	33892256
2-Deoxy-D-ribitol,1TMS,isomer #3	C[Si](C)(C)OC(CO)C(O)CCO	1437.1	Semi standard non polar	33892256
2-Deoxy-D-ribitol,1TMS,isomer #4	C[Si](C)(C)OCC(O)C(O)CCO	1439.1	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TMS,isomer #1	C[Si](C)(C)OCCC(O[Si](C)(C)C)C(O)CO	1512.4	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TMS,isomer #2	C[Si](C)(C)OCCC(O)C(CO)O[Si](C)(C)C	1539.5	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TMS,isomer #3	C[Si](C)(C)OCCC(O)C(O)CO[Si](C)(C)C	1552.9	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TMS,isomer #4	C[Si](C)(C)OC(CO)C(CCO)O[Si](C)(C)C	1508.1	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TMS,isomer #5	C[Si](C)(C)OCC(O)C(CCO)O[Si](C)(C)C	1529.7	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TMS,isomer #6	C[Si](C)(C)OCC(O[Si](C)(C)C)C(O)CCO	1532.9	Semi standard non polar	33892256
2-Deoxy-D-ribitol,3TMS,isomer #1	C[Si](C)(C)OCCC(O[Si](C)(C)C)C(CO)O[Si](C)(C)C	1582.7	Semi standard non polar	33892256
2-Deoxy-D-ribitol,3TMS,isomer #2	C[Si](C)(C)OCCC(O[Si](C)(C)C)C(O)CO[Si](C)(C)C	1588.1	Semi standard non polar	33892256
2-Deoxy-D-ribitol,3TMS,isomer #3	C[Si](C)(C)OCCC(O)C(CO[Si](C)(C)C)O[Si](C)(C)C	1606.9	Semi standard non polar	33892256
2-Deoxy-D-ribitol,3TMS,isomer #4	C[Si](C)(C)OCC(O[Si](C)(C)C)C(CCO)O[Si](C)(C)C	1575.0	Semi standard non polar	33892256
2-Deoxy-D-ribitol,4TMS,isomer #1	C[Si](C)(C)OCCC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O[Si](C)(C)C	1588.6	Semi standard non polar	33892256
2-Deoxy-D-ribitol,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCC(O)C(O)CO	1686.7	Semi standard non polar	33892256
2-Deoxy-D-ribitol,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(CCO)C(O)CO	1672.1	Semi standard non polar	33892256
2-Deoxy-D-ribitol,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(CO)C(O)CCO	1672.4	Semi standard non polar	33892256
2-Deoxy-D-ribitol,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OCC(O)C(O)CCO	1666.5	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCC(O[Si](C)(C)C(C)(C)C)C(O)CO	1967.1	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCCC(O)C(CO)O[Si](C)(C)C(C)(C)C	1967.0	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCCC(O)C(O)CO[Si](C)(C)C(C)(C)C	1976.7	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(CO)C(CCO)O[Si](C)(C)C(C)(C)C	1953.2	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OCC(O)C(CCO)O[Si](C)(C)C(C)(C)C	1961.3	Semi standard non polar	33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(O)CCO	1964.9	Semi standard non polar	33892256
2-Deoxy-D-ribitol,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCC(O[Si](C)(C)C(C)(C)C)C(CO)O[Si](C)(C)C(C)(C)C	2202.3	Semi standard non polar	33892256
2-Deoxy-D-ribitol,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCCC(O[Si](C)(C)C(C)(C)C)C(O)CO[Si](C)(C)C(C)(C)C	2209.1	Semi standard non polar	33892256
2-Deoxy-D-ribitol,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCCC(O)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2215.2	Semi standard non polar	33892256
2-Deoxy-D-ribitol,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CCO)O[Si](C)(C)C(C)(C)C	2197.0	Semi standard non polar	33892256
2-Deoxy-D-ribitol,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2423.0	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-D-ribitol GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-9000000000-839920e63ae81833c843	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Deoxy-D-ribitol GC-MS (4 TMS) - 70eV, Positive	splash10-0a4r-8239400000-e124927e21f7d46072cc	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Deoxy-D-ribitol 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-D-ribitol 10V, Positive-QTOF	splash10-014r-1900000000-1d6f0c49719625480ec0	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 20V, Positive-QTOF	splash10-0002-9400000000-930d72de6d5f26e844ff	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 40V, Positive-QTOF	splash10-0pba-9200000000-cfcf887fe98d3efc39ae	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 10V, Negative-QTOF	splash10-000i-3900000000-2700ddc4f5cfbb58b270	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 20V, Negative-QTOF	splash10-0551-9300000000-9cbfd49729ae70e723c7	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 40V, Negative-QTOF	splash10-0abm-9000000000-2c75d0978b923b706f82	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 10V, Negative-QTOF	splash10-0a4r-9600000000-27094c8c9dff7a6077d5	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 20V, Negative-QTOF	splash10-0a4i-9000000000-7d8d0517d4705455e257	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 40V, Negative-QTOF	splash10-052f-9000000000-fe53649d05e8056353de	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 10V, Positive-QTOF	splash10-0uxr-7900000000-f1f7bfd37043335b02c1	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 20V, Positive-QTOF	splash10-0k92-9300000000-2e0d55e703bfc59cd5da	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 40V, Positive-QTOF	splash10-0005-9000000000-60ddf91bc24f49a7d70c	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

FDB012117

KNApSAcK ID

C00055565

Chemspider ID

218353

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

249377

PDB ID

Not Available

ChEBI ID

Not Available

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-D-ribitol (HMDB0033919)

MOL for HMDB0033919 (2-Deoxy-D-ribitol)

3D MOL for HMDB0033919 (2-Deoxy-D-ribitol)

3D SDF for HMDB0033919 (2-Deoxy-D-ribitol)

3D-SDF for HMDB0033919 (2-Deoxy-D-ribitol)

PDB for HMDB0033919 (2-Deoxy-D-ribitol)

3D PDB for HMDB0033919 (2-Deoxy-D-ribitol)

SMILES for HMDB0033919 (2-Deoxy-D-ribitol)

INCHI for HMDB0033919 (2-Deoxy-D-ribitol)

Structure for HMDB0033919 (2-Deoxy-D-ribitol)

3D Structure for HMDB0033919 (2-Deoxy-D-ribitol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra