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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 00:44:23 UTC

Update Date

2023-02-21 17:26:55 UTC

HMDB ID

HMDB0039324

Secondary Accession Numbers

HMDB39324

Metabolite Identification

Common Name

xi-3-Hydroxy-2-oxobutanoic acid

Description

xi-3-Hydroxy-2-oxobutanoic acid, also known as 3-hydroxy-alpha-ketobutyrate or beta-hydroxy-alpha-oxobutyric acid, belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms. xi-3-Hydroxy-2-oxobutanoic acid has been detected, but not quantified in, fruits and milk and milk products. This could make XI-3-hydroxy-2-oxobutanoic acid a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on xi-3-Hydroxy-2-oxobutanoic acid.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
XI-3-hydroxy-2-oxobutanoate	Generator
3-Hydroxy-alpha-ketobutyrate	HMDB
beta-Hydroxy-alpha-oxobutyric acid	HMDB
beta-Hydroxy-alpha-ketobutyric acid	HMDB

Chemical Formula

C₄H₆O₄

Average Molecular Weight

118.088

Monoisotopic Molecular Weight

118.02660868

IUPAC Name

3-hydroxy-2-oxobutanoic acid

Traditional Name

3-hydroxy-2-oxobutanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C4H6O4/c1-2(5)3(6)4(7)8/h2,5H,1H3,(H,7,8)

InChI Key

QWZIITCYKKSZGN-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Short-chain keto acids and derivatives

Direct Parent

Short-chain keto acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Short-chain keto acid
Acyloin
Alpha-keto acid
Hydroxy acid
Monosaccharide
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Carbonyl group
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Alcohol
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0039324)
Cytoplasm (HMDB: HMDB0039324)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0039324)

Source

Exogenous

Exogenous (HMDB: HMDB0039324)

Food

Food (HMDB: HMDB0039324)

Fruit

Fruits (FooDB: FOOD00871)

Milk and milk product

Milk and milk products (FooDB: FOOD00863)

Endogenous

Plant

Plant (HMDB: HMDB0039324)

Animal

Animal (HMDB: HMDB0039324)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0039324)

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	178 g/L	ALOGPS
logP	-0.73	ALOGPS
logP	-0.18	ChemAxon
logS	0.18	ALOGPS
pKa (Strongest Acidic)	2.82	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	24.19 m³·mol⁻¹	ChemAxon
Polarizability	10.02 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]+	124.114	31661259
DarkChem	[M-H]-	118.917	31661259
DeepCCS	[M+H]+	123.544	30932474
DeepCCS	[M-H]-	120.744	30932474
DeepCCS	[M-2H]-	157.266	30932474
DeepCCS	[M+Na]+	131.995	30932474
AllCCS	[M+H]+	129.1	32859911
AllCCS	[M+H-H2O]+	124.9	32859911
AllCCS	[M+NH4]+	133.1	32859911
AllCCS	[M+Na]+	134.2	32859911
AllCCS	[M-H]-	121.1	32859911
AllCCS	[M+Na-2H]-	124.2	32859911
AllCCS	[M+HCOO]-	127.8	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.	1.79 minutes	32390414
Predicted by Siyang on May 30, 2022	9.9363 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.22 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	122.6 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1112.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	369.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	74.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	238.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	67.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	285.9 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	354.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	226.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	663.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	175.9 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	956.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	233.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	309.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	669.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	274.3 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	287.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
xi-3-Hydroxy-2-oxobutanoic acid	CC(O)C(=O)C(O)=O	2155.2	Standard polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid	CC(O)C(=O)C(O)=O	1492.1	Standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid	CC(O)C(=O)C(O)=O	964.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
xi-3-Hydroxy-2-oxobutanoic acid,1TMS,isomer #1	CC(O[Si](C)(C)C)C(=O)C(=O)O	1154.8	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,1TMS,isomer #2	CC(O)C(=O)C(=O)O[Si](C)(C)C	1066.1	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,1TMS,isomer #3	CC(O)=C(O[Si](C)(C)C)C(=O)O	1181.5	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,2TMS,isomer #1	CC(O[Si](C)(C)C)C(=O)C(=O)O[Si](C)(C)C	1270.5	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,2TMS,isomer #2	CC(O[Si](C)(C)C)=C(O[Si](C)(C)C)C(=O)O	1327.4	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,2TMS,isomer #3	CC(O)=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1280.4	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,3TMS,isomer #1	CC(O[Si](C)(C)C)=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1413.9	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,3TMS,isomer #1	CC(O[Si](C)(C)C)=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1388.2	Standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,1TBDMS,isomer #1	CC(O[Si](C)(C)C(C)(C)C)C(=O)C(=O)O	1424.3	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,1TBDMS,isomer #2	CC(O)C(=O)C(=O)O[Si](C)(C)C(C)(C)C	1317.1	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,1TBDMS,isomer #3	CC(O)=C(O[Si](C)(C)C(C)(C)C)C(=O)O	1456.4	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,2TBDMS,isomer #1	CC(O[Si](C)(C)C(C)(C)C)C(=O)C(=O)O[Si](C)(C)C(C)(C)C	1701.8	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,2TBDMS,isomer #2	CC(O[Si](C)(C)C(C)(C)C)=C(O[Si](C)(C)C(C)(C)C)C(=O)O	1793.6	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,2TBDMS,isomer #3	CC(O)=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1758.5	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,3TBDMS,isomer #1	CC(O[Si](C)(C)C(C)(C)C)=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2039.2	Semi standard non polar	33892256
xi-3-Hydroxy-2-oxobutanoic acid,3TBDMS,isomer #1	CC(O[Si](C)(C)C(C)(C)C)=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2007.6	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dm-9000000000-c5fcc422fa0de530d8a9	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid GC-MS (2 TMS) - 70eV, Positive	splash10-00kb-7910000000-118df9503ad80c5dabfa	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-3-Hydroxy-2-oxobutanoic 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 - xi-3-Hydroxy-2-oxobutanoic acid 10V, Positive-QTOF	splash10-0uxr-2900000000-b864e37d7498e32681b1	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 20V, Positive-QTOF	splash10-0udi-9700000000-e0b4b333a76700a2250d	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 40V, Positive-QTOF	splash10-0a4i-9100000000-f1040853a7d12574a6d3	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 10V, Negative-QTOF	splash10-00xr-9500000000-8c48669b820611f80189	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 20V, Negative-QTOF	splash10-00di-9000000000-b1522273ffa241be6af6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 40V, Negative-QTOF	splash10-05fr-9000000000-318256d0a438b723a0f9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 10V, Positive-QTOF	splash10-0002-9000000000-02daccae6dd59f82b8ad	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 20V, Positive-QTOF	splash10-0002-9000000000-00ba25458eb6c0cc2940	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 40V, Positive-QTOF	splash10-0002-9000000000-db8c4c2ec1add8b902ff	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 10V, Negative-QTOF	splash10-05fr-9000000000-2dcd2f20c9e98cde083e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 20V, Negative-QTOF	splash10-0ab9-9000000000-e1010e724cd2da8b00e0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-3-Hydroxy-2-oxobutanoic acid 40V, Negative-QTOF	splash10-0a4i-9000000000-9a36623c9b9dd9c6afd1	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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX 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

FDB018877

KNApSAcK ID

Not Available

Chemspider ID

164189

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

188958

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 xi-3-Hydroxy-2-oxobutanoic acid (HMDB0039324)

MOL for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

3D MOL for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

3D SDF for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

3D-SDF for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

PDB for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

3D PDB for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

SMILES for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

INCHI for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

Structure for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

3D Structure for HMDB0039324 (xi-3-Hydroxy-2-oxobutanoic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra