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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

2006-05-22 14:17:53 UTC

Update Date

2023-02-21 17:16:24 UTC

HMDB ID

HMDB0002453

Secondary Accession Numbers

HMDB02453

Metabolite Identification

Common Name

4-Deoxythreonic acid

Description

4-Deoxythreonic acid, also known as 4-deoxythreonate, belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. 4-Deoxythreonic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 4-deoxythreonic acid a potential biomarker for the consumption of these foods. 4-Deoxythreonic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on 4-Deoxythreonic 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
4-Deoxythreonate	Generator
(+/-)-erythro-2,3-dihydroxybutyrate	HMDB
(+/-)-erythro-2,3-dihydroxybutyric acid	HMDB
(2R,3S)-Rel-2,3-dihydroxy--butanoate	HMDB
(2R,3S)-Rel-2,3-dihydroxy--butanoic acid	HMDB
(R,s)-2,3-dihydroxybutanoate	HMDB
(R,s)-2,3-dihydroxybutanoic acid	HMDB
2,3-threo-Dihydroxybutyrate	HMDB
2,3-threo-Dihydroxybutyric acid	HMDB
4-Deoxy-threonate	HMDB
4-Deoxy-threonic acid	HMDB
erythro-2,3-Dihydroxybutyrate	HMDB
erythro-2,3-Dihydroxybutyric acid	HMDB

Chemical Formula

C₄H₈O₄

Average Molecular Weight

120.1039

Monoisotopic Molecular Weight

120.042258744

IUPAC Name

(2S,3R)-2,3-dihydroxybutanoic acid

Traditional Name

4-deoxythreonic acid

CAS Registry Number

5057-93-2

SMILES

C[C@@H](O)[C@H](O)C(O)=O

InChI Identifier

InChI=1S/C4H8O4/c1-2(5)3(6)4(7)8/h2-3,5-6H,1H3,(H,7,8)/t2-,3+/m1/s1

InChI Key

LOUGYXZSURQALL-GBXIJSLDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Short-chain hydroxy acid
Sugar acid
Monosaccharide
Hydroxy acid
Alpha-hydroxy acid
Fatty acid
Secondary alcohol
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2,3-dihydroxybutanoic acid (CHEBI:86391 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0002453)

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0002453)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0002453)

Source

Endogenous

Endogenous (HMDB: HMDB0002453)

Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)
Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)

Equine

Horse (FooDB: FOOD00378)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

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	454 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-1.1	ChemAxon
logS	0.58	ALOGPS
pKa (Strongest Acidic)	3.63	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	24.8 m³·mol⁻¹	ChemAxon
Polarizability	10.72 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]+	127.173	31661259
DarkChem	[M-H]-	122.062	31661259
DeepCCS	[M+H]+	124.254	30932474
DeepCCS	[M-H]-	120.551	30932474
DeepCCS	[M-2H]-	157.903	30932474
DeepCCS	[M+Na]+	133.315	30932474
AllCCS	[M+H]+	130.7	32859911
AllCCS	[M+H-H2O]+	126.5	32859911
AllCCS	[M+NH4]+	134.6	32859911
AllCCS	[M+Na]+	135.7	32859911
AllCCS	[M-H]-	122.1	32859911
AllCCS	[M+Na-2H]-	125.3	32859911
AllCCS	[M+HCOO]-	128.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
4-Deoxythreonic acid	C[C@@H](O)[C@H](O)C(O)=O	2364.8	Standard polar	33892256
4-Deoxythreonic acid	C[C@@H](O)[C@H](O)C(O)=O	1077.2	Standard non polar	33892256
4-Deoxythreonic acid	C[C@@H](O)[C@H](O)C(O)=O	1120.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
4-Deoxythreonic acid,1TMS,isomer #1	C[C@@H](O[Si](C)(C)C)[C@H](O)C(=O)O	1173.6	Semi standard non polar	33892256
4-Deoxythreonic acid,1TMS,isomer #2	C[C@@H](O)[C@H](O[Si](C)(C)C)C(=O)O	1195.1	Semi standard non polar	33892256
4-Deoxythreonic acid,1TMS,isomer #3	C[C@@H](O)[C@H](O)C(=O)O[Si](C)(C)C	1112.6	Semi standard non polar	33892256
4-Deoxythreonic acid,2TMS,isomer #1	C[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)C(=O)O	1283.2	Semi standard non polar	33892256
4-Deoxythreonic acid,2TMS,isomer #2	C[C@@H](O[Si](C)(C)C)[C@H](O)C(=O)O[Si](C)(C)C	1246.8	Semi standard non polar	33892256
4-Deoxythreonic acid,2TMS,isomer #3	C[C@@H](O)[C@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1249.8	Semi standard non polar	33892256
4-Deoxythreonic acid,3TMS,isomer #1	C[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1361.8	Semi standard non polar	33892256
4-Deoxythreonic acid,1TBDMS,isomer #1	C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)C(=O)O	1435.4	Semi standard non polar	33892256
4-Deoxythreonic acid,1TBDMS,isomer #2	C[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O	1453.3	Semi standard non polar	33892256
4-Deoxythreonic acid,1TBDMS,isomer #3	C[C@@H](O)[C@H](O)C(=O)O[Si](C)(C)C(C)(C)C	1342.4	Semi standard non polar	33892256
4-Deoxythreonic acid,2TBDMS,isomer #1	C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O	1743.5	Semi standard non polar	33892256
4-Deoxythreonic acid,2TBDMS,isomer #2	C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)C(=O)O[Si](C)(C)C(C)(C)C	1690.7	Semi standard non polar	33892256
4-Deoxythreonic acid,2TBDMS,isomer #3	C[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1693.1	Semi standard non polar	33892256
4-Deoxythreonic acid,3TBDMS,isomer #1	C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1996.5	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 - 4-Deoxythreonic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-002g-9000000000-4f8b3914e68986e2fc76	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxythreonic acid GC-MS (3 TMS) - 70eV, Positive	splash10-01b9-7594000000-41795a8299b4ed9a75dc	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 4-Deoxythreonic 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 - 4-Deoxythreonic acid 10V, Positive-QTOF	splash10-0uk9-3900000000-5fd7ebfcf6875e23274a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 20V, Positive-QTOF	splash10-0umr-9500000000-6fef2d02f632a0eefd83	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 40V, Positive-QTOF	splash10-0a4r-9000000000-825548e71f4decf6fa07	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 10V, Negative-QTOF	splash10-016r-9700000000-c98992a42c3b24d2b299	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 20V, Negative-QTOF	splash10-05di-9100000000-15421a37ae239a136cea	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 40V, Negative-QTOF	splash10-0ab9-9000000000-bdc0f45a587e25111ed4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 10V, Negative-QTOF	splash10-00or-9800000000-2fbe96770b983d31a58d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 20V, Negative-QTOF	splash10-004l-9000000000-a0881fec62969be92bad	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 40V, Negative-QTOF	splash10-0a4l-9000000000-16140d690957c073bf98	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 10V, Positive-QTOF	splash10-0002-9200000000-794a2a36a438372a84c3	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 20V, Positive-QTOF	splash10-0a4j-9000000000-1db4f99bbccdd36ec8b0	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-Deoxythreonic acid 40V, Positive-QTOF	splash10-0002-9000000000-488ae4d8cef018c0dfe1	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Detected and Quantified	12.3 (4.4-19.8) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	14.0 +/- 7.0 umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	25.0 +/- 10.0 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	18.2 (5.6-23.9) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	307.674 +/- 224.458 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	Analysis of 30 no...	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	28157703	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected and Quantified	442.222 +/- 291.319 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	Analysis of 30 no...	details
Urine	Detected and Quantified	765.086 +/- 469.712 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Gastroesophageal reflux disease	Analysis of 30 no...	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Bladder cancer	28157703	details

Associated Disorders and Diseases

Disease References

Eosinophilic esophagitis
Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.

Associated OMIM IDs

610247 (Eosinophilic esophagitis)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023007

KNApSAcK ID

C00052154

Chemspider ID

9139682

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6686

PubChem Compound

10964471

PDB ID

Not Available

ChEBI ID

86391

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Sakai, Takashi; Nakamura, Toshiki; Fukuda, Katsuyoshi; Amano, Eiichiro; Utaka, Masanori; Takeda, Akira. Highly enantioselective reduction of ethyl 2-acyloxy-3-oxobutanoate with immobilized bakers' yeast. Bulletin of the Chemical Society of Japan (1986), 59(10), 3185-8.

Material Safety Data Sheet (MSDS)

Not Available

General References

Kassel DB, Martin M, Schall W, Sweeley CC: Urinary metabolites of L-threonine in type 1 diabetes determined by combined gas chromatography/chemical ionization mass spectrometry. Biomed Environ Mass Spectrom. 1986 Oct;13(10):535-40. [PubMed:2947647 ]
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 ]
Tuchman M, Bowers LD, Fregien KD, Crippin PJ, Krivit W: Capillary gas chromatographic separation of urinary organic acids. Retention indices of 101 urinary acids on a 5% phenylmethyl silicone capillary column. J Chromatogr Sci. 1984 May;22(5):198-202. [PubMed:6725493 ]
Maeda K, Shiraishi S, Sakamoto N, Ohki T, Hosoi M, Ohta K, Yamanaka N: Identification of Escherichia coli by detection of hydroquinone and uracil in the urine system. J Chromatogr. 1985 Nov 29;345(1):11-8. [PubMed:3910670 ]

Showing metabocard for 4-Deoxythreonic acid (HMDB0002453)

MOL for HMDB0002453 (4-Deoxythreonic acid)

3D MOL for HMDB0002453 (4-Deoxythreonic acid)

3D SDF for HMDB0002453 (4-Deoxythreonic acid)

3D-SDF for HMDB0002453 (4-Deoxythreonic acid)

PDB for HMDB0002453 (4-Deoxythreonic acid)

3D PDB for HMDB0002453 (4-Deoxythreonic acid)

SMILES for HMDB0002453 (4-Deoxythreonic acid)

INCHI for HMDB0002453 (4-Deoxythreonic acid)

Structure for HMDB0002453 (4-Deoxythreonic acid)

3D Structure for HMDB0002453 (4-Deoxythreonic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra