MiMeDB: Showing metabocard for 2-dehydro-3-deoxy-D-arabinonate (MMDBc0054162)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:56:36 UTC

Update Date

2025-10-07 16:08:24 UTC

Metabolite ID

MMDBc0054162

Metabolite Identification

Common Name

2-dehydro-3-deoxy-D-arabinonate

Description

2-dehydro-3-deoxy-D-arabinonate is a carbohydrate derivative. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(4S)-4,5-Dihydroxy-2-oxopentanoate	ChEBI
2-Dehydro-3-deoxy-D-arabinonate	ChEBI
2-Dehydro-3-deoxy-D-pentonate	ChEBI
2-Dehydro-3-deoxy-D-xylonate	ChEBI
(4S)-4,5-Dihydroxy-2-oxopentanoic acid	Generator
2-Dehydro-3-deoxy-D-pentonic acid	Generator
2-Dehydro-3-deoxy-D-xylonic acid	Generator
2-dehydro-3-Deoxy-D-arabinonic acid	Generator

Molecular Formula

C₅H₈O₅

Average Mass

148.114

Monoisotopic Mass

148.037173358

IUPAC Name

(4S)-4,5-dihydroxy-2-oxopentanoic acid

Traditional Name

2-dehydro-3-deoxy-D-pentonate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H8O5/c6-2-3(7)1-4(8)5(9)10/h3,6-7H,1-2H2,(H,9,10)/t3-/m0/s1

InChI Key

UQIGQRSJIKIPKZ-VKHMYHEASA-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

Short-chain keto acid
Alpha-keto acid
Beta-hydroxy ketone
Alpha-hydroxy ketone
1,2-diol
Ketone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2-oxo monocarboxylic acid (CHEBI:1060 )
5-hydroxy monocarboxylic acid (CHEBI:1060 )
ketoaldonic acid (CHEBI:1060 )
pentonic acid (CHEBI:1060 )
4-hydroxy monocarboxylic acid (CHEBI:1060 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	205 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-1.1	ChemAxon
logS	0.14	ALOGPS
pKa (Strongest Acidic)	2.91	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	30.35 m³·mol⁻¹	ChemAxon
Polarizability	12.91 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001j-1900000000-7c4078f70341043b1d49	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03e9-9800000000-57deed0b91cef534b1d4	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0abc-9000000000-b2ed0ef20cca6d3c4092	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-3900000000-8b7d0f3c7532996a7ca5	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fki-9400000000-c4ebc2e5bd6cced658df	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05g3-9000000000-3847a7aaf37af54b668d	2019-02-23	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	280.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	247.8
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	52.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	246.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	262.4
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	326.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	753.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	662.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	830.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	171.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	296.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	192.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	49.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	337.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	659.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	64.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	210.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	837.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	591.3

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_1	C[Si](C)(C)OC[C@@H](O)CC(=O)C(=O)O	standard non polar	2025-10-24	1697.95
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_2	C[Si](C)(C)O[C@H](CO)CC(=O)C(=O)O	standard non polar	2025-10-24	1893.06
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_3	C[Si](C)(C)OC(=O)C(=O)C[C@H](O)CO	standard non polar	2025-10-24	2021.11
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_4	C[Si](C)(C)OC(=C[C@H](O)CO)C(=O)O	standard non polar	2025-10-24	2029.38
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_5	C[Si](C)(C)OC[C@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	2003.56
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_6	C[Si](C)(C)OC[C@@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2716.0
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_7	C[Si](C)(C)OC[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	2693.97
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_8	C[Si](C)(C)OC(=O)C(=O)C[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	2072.89
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_9	C[Si](C)(C)OC(=C[C@@H](CO)O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1988.92
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_10	C[Si](C)(C)OC(=O)C(=C[C@H](O)CO)O[Si](C)(C)C	standard non polar	2025-10-24	2025.17
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_11	C[Si](C)(C)OC[C@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2063.1
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_12	C[Si](C)(C)OC[C@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	1347.46
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_13	C[Si](C)(C)OC[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2325.7
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_14	C[Si](C)(C)OC(=O)C(=C[C@@H](CO)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1922.32
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_15	C[Si](C)(C)OC[C@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1391.38
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_1	C[Si](C)(C)OC[C@@H](O)CC(=O)C(=O)O	standard polar	2025-10-24	2434.23
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_2	C[Si](C)(C)O[C@H](CO)CC(=O)C(=O)O	standard polar	2025-10-24	2198.86
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_3	C[Si](C)(C)OC(=O)C(=O)C[C@H](O)CO	standard polar	2025-10-24	2029.54
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_4	C[Si](C)(C)OC(=C[C@H](O)CO)C(=O)O	standard polar	2025-10-24	1916.53
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_5	C[Si](C)(C)OC[C@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	2108.35
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_6	C[Si](C)(C)OC[C@@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2272.97
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_7	C[Si](C)(C)OC[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2085.07
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_8	C[Si](C)(C)OC(=O)C(=O)C[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	1894.02
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_9	C[Si](C)(C)OC(=C[C@@H](CO)O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2535.23
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_10	C[Si](C)(C)OC(=O)C(=C[C@H](O)CO)O[Si](C)(C)C	standard polar	2025-10-24	1620.71
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_11	C[Si](C)(C)OC[C@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1970.18
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_12	C[Si](C)(C)OC[C@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	2087.59
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_13	C[Si](C)(C)OC[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2695.69
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_14	C[Si](C)(C)OC(=O)C(=C[C@@H](CO)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1585.91
Gas Chromatography	2-dehydro-3-deoxy-D-arabinonate_TMS_15	C[Si](C)(C)OC[C@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2617.2

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species
Archaea/Archaea	Euryarchaeota	1
Bacteria/Eubacteria	Proteobacteria	1
Bacteria	Proteobacteria	1
Archaea	Crenarchaeota	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

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

C03826

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

1060

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 2-dehydro-3-deoxy-D-arabinonate (MMDBc0054162)

MOL for #<Metabolite:0x000056432046a0c8>

3D MOL for #<Metabolite:0x000056432046a0c8>

3D SDF for #<Metabolite:0x000056432046a0c8>

3D-SDF for #<Metabolite:0x000056432046a0c8>

PDB for #<Metabolite:0x000056432046a0c8>

3D PDB for #<Metabolite:0x000056432046a0c8>

SMILES for #<Metabolite:0x000056432046a0c8>

INCHI for #<Metabolite:0x000056432046a0c8>

Structure for #<Metabolite:0x000056432046a0c8>

3D Structure for #<Metabolite:0x000056432046a0c8>