MiMeDB: Showing metabocard for (R)-2,3-Dihydroxy-3-methylbutanoate (MMDBc0033208)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:39:07 UTC

Update Date

2025-10-07 16:07:57 UTC

Metabolite ID

MMDBc0033208

Metabolite Identification

Common Name

(R)-2,3-Dihydroxy-3-methylbutanoate

Description

(R)-2,3-Dihydroxy-3-methylbutanoate is a carbohydrate-derived metabolite. There is limited literature available on this compound, indicating a need for further research to elucidate its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2R)-2,3-Dihydroxy-3-methylbutanoate	ChEBI
(R)-2,3-Dihydroxy-isovalerate	ChEBI
(2R)-2,3-Dihydroxy-3-methylbutanoic acid	Generator
(R)-2,3-Dihydroxy-isovaleric acid	Generator
(R)-2,3-Dihydroxy-3-methylbutanoic acid	Generator

Molecular Formula

C₅H₉O₄

Average Mass

133.1226

Monoisotopic Mass

133.050083776

IUPAC Name

(2R)-2,3-dihydroxy-3-methylbutanoate

Traditional Name

(R)-2,3-dihydroxy-isovalerate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H10O4/c1-5(2,9)3(6)4(7)8/h3,6,9H,1-2H3,(H,7,8)/p-1/t3-/m0/s1

InChI Key

JTEYKUFKXGDTEU-VKHMYHEASA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Branched fatty acid
Hydroxy fatty acid
Short-chain hydroxy acid
Methyl-branched fatty acid
Monosaccharide
Tertiary alcohol
Secondary alcohol
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2,3-dihydroxy-3-methylbutanoate (CHEBI:49072 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	717 g/L	ALOGPS
logP	-0.72	ALOGPS
logP	-0.82	ChemAxon
logS	0.68	ALOGPS
pKa (Strongest Acidic)	3.8	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	80.59 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	40.28 m³·mol⁻¹	ChemAxon
Polarizability	12.06 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00lr-2900000000-a99366332947599a82dd	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0gi3-9800000000-01b2a28ddcd8adde4089	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9100000000-25163fa3e081d6f5104b	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00m0-6900000000-8b862e81d76dceb2fd8c	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01b9-9700000000-6f02fcfaadc259734d5b	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00dr-9100000000-90062a20d25ab5bcbef8	2016-09-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	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	257.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	89.6
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	148.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	351.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	300.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	345.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	999.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	115.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	677.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	226.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	279.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	197.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	76.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	224.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	516.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	47.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	271.0
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	860.9
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	644.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(R)-2,3-Dihydroxy-3-methylbutanoate_TMS_1	CC(C)(O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	1837.72
Gas Chromatography	(R)-2,3-Dihydroxy-3-methylbutanoate_TMS_2	CC(C)(O)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1750.8
Gas Chromatography	(R)-2,3-Dihydroxy-3-methylbutanoate_TMS_3	CC(C)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	2156.98
Gas Chromatography	(R)-2,3-Dihydroxy-3-methylbutanoate_TMS_1	CC(C)(O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	1997.02
Gas Chromatography	(R)-2,3-Dihydroxy-3-methylbutanoate_TMS_2	CC(C)(O)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2296.63
Gas Chromatography	(R)-2,3-Dihydroxy-3-methylbutanoate_TMS_3	CC(C)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2106.27

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Firmicutes	260	Human feces; Human pleural fluid plaque; Pig ; Human ; Human subgingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	173	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	111	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	83	Human feces; Human appendix biopsy; Human ; Human saliva; Human gastric fluid; Human urine	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	7	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23615351

PDB ID

Not Available

ChEBI ID

49072

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for (R)-2,3-Dihydroxy-3-methylbutanoate (MMDBc0033208)

MOL for #<Metabolite:0x00007f9ab4c2ec90>

3D MOL for #<Metabolite:0x00007f9ab4c2ec90>

3D SDF for #<Metabolite:0x00007f9ab4c2ec90>

3D-SDF for #<Metabolite:0x00007f9ab4c2ec90>

PDB for #<Metabolite:0x00007f9ab4c2ec90>

3D PDB for #<Metabolite:0x00007f9ab4c2ec90>

SMILES for #<Metabolite:0x00007f9ab4c2ec90>

INCHI for #<Metabolite:0x00007f9ab4c2ec90>

Structure for #<Metabolite:0x00007f9ab4c2ec90>

3D Structure for #<Metabolite:0x00007f9ab4c2ec90>