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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-02-26 19:02:16 UTC

Update Date

2022-03-07 03:17:36 UTC

HMDB ID

HMDB0059753

Secondary Accession Numbers

HMDB59753

Metabolite Identification

Common Name

2-Deoxypentonic acid

Description

2-Deoxypentonic acid, also known as 2-deoxypentonate, belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. 2-Deoxypentonic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). These are fatty acids in which the chain bears an hydroxyl group.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-Deoxypentonate	Generator
3,4,5-Trihydroxypentanoate	Generator

Chemical Formula

C₅H₁₀O₅

Average Molecular Weight

150.1299

Monoisotopic Molecular Weight

150.05282343

IUPAC Name

3,4,5-trihydroxypentanoic acid

Traditional Name

3,4,5-trihydroxypentanoic acid

CAS Registry Number

Not Available

SMILES

OCC(O)C(O)CC(O)=O

InChI Identifier

InChI=1S/C5H10O5/c6-2-4(8)3(7)1-5(9)10/h3-4,6-8H,1-2H2,(H,9,10)

InChI Key

VBUWJOHKCBQXNU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Beta hydroxy acids and derivatives

Direct Parent

Beta hydroxy acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Short-chain hydroxy acid
Fatty acid
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Polyol
Organooxygen compound
Organic oxygen compound
Alcohol
Carbonyl group
Primary alcohol
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Urine (PMID: 949837)

Process

Not Available

Role

Not Available

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	511 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.1	ChemAxon
logS	0.53	ALOGPS
pKa (Strongest Acidic)	4.03	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	30.97 m³·mol⁻¹	ChemAxon
Polarizability	13.52 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]+	133.074	31661259
DarkChem	[M-H]-	126.938	31661259
DeepCCS	[M+H]+	128.491	30932474
DeepCCS	[M-H]-	125.438	30932474
DeepCCS	[M-2H]-	161.915	30932474
DeepCCS	[M+Na]+	137.078	30932474
AllCCS	[M+H]+	135.3	32859911
AllCCS	[M+H-H2O]+	131.3	32859911
AllCCS	[M+NH4]+	139.0	32859911
AllCCS	[M+Na]+	140.0	32859911
AllCCS	[M-H]-	127.3	32859911
AllCCS	[M+Na-2H]-	129.5	32859911
AllCCS	[M+HCOO]-	132.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Deoxypentonic acid	OCC(O)C(O)CC(O)=O	3142.2	Standard polar	33892256
2-Deoxypentonic acid	OCC(O)C(O)CC(O)=O	1400.1	Standard non polar	33892256
2-Deoxypentonic acid	OCC(O)C(O)CC(O)=O	1458.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Deoxypentonic acid,1TMS,isomer #1	C[Si](C)(C)OCC(O)C(O)CC(=O)O	1547.0	Semi standard non polar	33892256
2-Deoxypentonic acid,1TMS,isomer #2	C[Si](C)(C)OC(CO)C(O)CC(=O)O	1556.5	Semi standard non polar	33892256
2-Deoxypentonic acid,1TMS,isomer #3	C[Si](C)(C)OC(CC(=O)O)C(O)CO	1520.0	Semi standard non polar	33892256
2-Deoxypentonic acid,1TMS,isomer #4	C[Si](C)(C)OC(=O)CC(O)C(O)CO	1539.5	Semi standard non polar	33892256
2-Deoxypentonic acid,2TMS,isomer #1	C[Si](C)(C)OCC(O[Si](C)(C)C)C(O)CC(=O)O	1621.3	Semi standard non polar	33892256
2-Deoxypentonic acid,2TMS,isomer #2	C[Si](C)(C)OCC(O)C(CC(=O)O)O[Si](C)(C)C	1602.1	Semi standard non polar	33892256
2-Deoxypentonic acid,2TMS,isomer #3	C[Si](C)(C)OCC(O)C(O)CC(=O)O[Si](C)(C)C	1598.0	Semi standard non polar	33892256
2-Deoxypentonic acid,2TMS,isomer #4	C[Si](C)(C)OC(CO)C(CC(=O)O)O[Si](C)(C)C	1589.2	Semi standard non polar	33892256
2-Deoxypentonic acid,2TMS,isomer #5	C[Si](C)(C)OC(=O)CC(O)C(CO)O[Si](C)(C)C	1597.0	Semi standard non polar	33892256
2-Deoxypentonic acid,2TMS,isomer #6	C[Si](C)(C)OC(=O)CC(O[Si](C)(C)C)C(O)CO	1551.5	Semi standard non polar	33892256
2-Deoxypentonic acid,3TMS,isomer #1	C[Si](C)(C)OCC(O[Si](C)(C)C)C(CC(=O)O)O[Si](C)(C)C	1667.0	Semi standard non polar	33892256
2-Deoxypentonic acid,3TMS,isomer #2	C[Si](C)(C)OCC(O[Si](C)(C)C)C(O)CC(=O)O[Si](C)(C)C	1663.5	Semi standard non polar	33892256
2-Deoxypentonic acid,3TMS,isomer #3	C[Si](C)(C)OCC(O)C(CC(=O)O[Si](C)(C)C)O[Si](C)(C)C	1648.1	Semi standard non polar	33892256
2-Deoxypentonic acid,3TMS,isomer #4	C[Si](C)(C)OC(=O)CC(O[Si](C)(C)C)C(CO)O[Si](C)(C)C	1636.1	Semi standard non polar	33892256
2-Deoxypentonic acid,4TMS,isomer #1	C[Si](C)(C)OCC(O[Si](C)(C)C)C(CC(=O)O[Si](C)(C)C)O[Si](C)(C)C	1677.3	Semi standard non polar	33892256
2-Deoxypentonic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(O)C(O)CC(=O)O	1809.2	Semi standard non polar	33892256
2-Deoxypentonic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(CO)C(O)CC(=O)O	1817.9	Semi standard non polar	33892256
2-Deoxypentonic acid,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(CC(=O)O)C(O)CO	1783.6	Semi standard non polar	33892256
2-Deoxypentonic acid,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)CC(O)C(O)CO	1772.4	Semi standard non polar	33892256
2-Deoxypentonic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(O)CC(=O)O	2103.8	Semi standard non polar	33892256
2-Deoxypentonic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(O)C(CC(=O)O)O[Si](C)(C)C(C)(C)C	2068.6	Semi standard non polar	33892256
2-Deoxypentonic acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC(O)C(O)CC(=O)O[Si](C)(C)C(C)(C)C	2036.7	Semi standard non polar	33892256
2-Deoxypentonic acid,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(CO)C(CC(=O)O)O[Si](C)(C)C(C)(C)C	2054.7	Semi standard non polar	33892256
2-Deoxypentonic acid,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC(=O)CC(O)C(CO)O[Si](C)(C)C(C)(C)C	2032.1	Semi standard non polar	33892256
2-Deoxypentonic acid,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OC(=O)CC(O[Si](C)(C)C(C)(C)C)C(O)CO	2006.5	Semi standard non polar	33892256
2-Deoxypentonic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CC(=O)O)O[Si](C)(C)C(C)(C)C	2312.4	Semi standard non polar	33892256
2-Deoxypentonic acid,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(O)CC(=O)O[Si](C)(C)C(C)(C)C	2297.4	Semi standard non polar	33892256
2-Deoxypentonic acid,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC(O)C(CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2280.4	Semi standard non polar	33892256
2-Deoxypentonic acid,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)CC(O[Si](C)(C)C(C)(C)C)C(CO)O[Si](C)(C)C(C)(C)C	2268.7	Semi standard non polar	33892256
2-Deoxypentonic acid,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2482.4	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-Deoxypentonic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-06sc-9000000000-c78de6841f3acf1fa76b	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Deoxypentonic acid GC-MS (4 TMS) - 70eV, Positive	splash10-00g0-9027200000-adc32665fe9b412fb0fb	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Deoxypentonic acid 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-Deoxypentonic acid 10V, Positive-QTOF	splash10-001i-1900000000-abab4e4ee07915ad25df	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 20V, Positive-QTOF	splash10-07cu-9700000000-56ec7d5976e902370580	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 40V, Positive-QTOF	splash10-06xx-9000000000-cb82a1f13b50d91492bd	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 10V, Negative-QTOF	splash10-052b-3900000000-0b54ad95ab8a0e82a5a0	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 20V, Negative-QTOF	splash10-0a4r-9300000000-1190b2589b795883f41c	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 40V, Negative-QTOF	splash10-0a4l-9000000000-6a9184456a482fb916e1	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 10V, Negative-QTOF	splash10-0a4j-3900000000-a9aa746c80102cdac126	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 20V, Negative-QTOF	splash10-0a4l-9000000000-9dafbd8baf4cb85faab2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 40V, Negative-QTOF	splash10-0006-9000000000-01325c407d88a7a20632	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 10V, Positive-QTOF	splash10-00li-7900000000-a34eed2d06f591b7cbbd	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 20V, Positive-QTOF	splash10-00xv-9300000000-8da3691bcbc57bad1a6c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 40V, Positive-QTOF	splash10-0006-9000000000-7a979d2ff58310d5e57c	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	949837	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	Not Available	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	Not Available	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Normal	Not Available	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Normal	Not Available	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Normal	Not Available	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13871872

PDB ID

Not Available

ChEBI ID

89890

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

Not Available

Showing metabocard for 2-Deoxypentonic acid (HMDB0059753)

MOL for HMDB0059753 (2-Deoxypentonic acid)

3D MOL for HMDB0059753 (2-Deoxypentonic acid)

3D SDF for HMDB0059753 (2-Deoxypentonic acid)

3D-SDF for HMDB0059753 (2-Deoxypentonic acid)

PDB for HMDB0059753 (2-Deoxypentonic acid)

3D PDB for HMDB0059753 (2-Deoxypentonic acid)

SMILES for HMDB0059753 (2-Deoxypentonic acid)

INCHI for HMDB0059753 (2-Deoxypentonic acid)

Structure for HMDB0059753 (2-Deoxypentonic acid)

3D Structure for HMDB0059753 (2-Deoxypentonic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra