Human Metabolome Database: Showing metabocard for (R)-2,3-Dihydroxy-isovalerate (HMDB0012141)

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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2009-04-06 16:19:54 UTC

Update Date

2020-02-26 21:36:58 UTC

HMDB ID

HMDB0012141

Secondary Accession Numbers

HMDB12141

Metabolite Identification

Common Name

(R)-2,3-Dihydroxy-isovalerate

Description

(R) 2,3-Dihydroxy-isovalerate is an intermediate in valine, leucine and isoleucine biosynthesis. The pathway of valine biosynthesis is a four-step pathway that shares all of its steps with the parallel pathway of isoleucine biosynthesis. These entwined pathways are part of the superpathway of leucine, valine, and isoleucine biosynthesis , that generates not only isoleucine and valine, but also leucine. (R) 2,3-Dihydroxy-isovalerate is generated from 3-Hydroxy-3-methyl-2-oxobutanoic acid via the enzyme ketol-acid reductoisomerase (EC 1.1.1.86) then it is converted to 2-Oxoisovalerate via the dihydroxy-acid dehydratase (EC:4.2.1.9).

Structure

MOL SDF PDB SMILES InChI

Synonyms

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

Chemical Formula

C₅H₁₀O₄

Average Molecular Weight

134.1305

Monoisotopic Molecular Weight

134.057908808

IUPAC Name

(2R)-2,3-dihydroxy-3-methylbutanoic acid

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)/t3-/m0/s1

InChI Key

JTEYKUFKXGDTEU-VKHMYHEASA-N

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2,3-dihydroxy-3-methylbutanoic acid (CHEBI:15684 )

Ontology

Ingestion

Biological location:

Subcellular:

Biofluid and excreta:

Source:

Biological:

Animal

Process

Naturally occurring process:

Biological process:

Biochemical process:

Biochemical pathway:

Lipid metabolism pathway

Chemical reaction:

Lipid peroxidation

Role

Biological role:

Physical Properties

State

Solid

Experimental 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

Predicted Properties

Property	Value	Source
Water Solubility	529 g/L	ALOGPS
logP	-0.83	ALOGPS
logP	-0.82	ChemAxon
logS	0.6	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	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	29.44 m³·mol⁻¹	ChemAxon
Polarizability	12.48 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	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-9000000000-59e6990530d950227520	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00s9-9473000000-9708bfc20ee5ae043678	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-4900000000-196ffbbf313a33f24f27	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00ri-9300000000-aebebbbe2c7c11465a67	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-92af6a04d8cb7601ab35	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0019-9500000000-2837622949a6bd688094	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00s9-9400000000-0fc7aa81197fc5feb444	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00dr-9000000000-45f3b95b2f30ea8445c1	Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces
Saliva
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Normal	25037050	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Normal	22308371	details
Urine	Detected and Quantified	<25 umol/mmol creatinine	Not Specified	Not Specified	Normal	26163321	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Metastatic melanoma	28923537	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Attachment loss	31026179	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Missing teeth	31026179	details
Saliva	Detected but not Quantified		Adult (>18 years old)	Male	Periodontal Probing Depth	31026179	details
Urine	Detected but not Quantified		Adult (>18 years old)	Both	Bladder cancer	28157703	details
Urine	Detected and Quantified	782-2500 umol/mmol creatinine	Infant (0-1 year old)	Both	Short-chain enoyl-CoA hydratase deficiency	26163321	details
Urine	Detected and Quantified	27-406 umol/mmol creatinine	Not Specified	Not Specified	Methylmalonyl-CoA mutase deficiency	26163321	details
Urine	Detected and Quantified	82-187 umol/mmol creatinine	Not Specified	Not Specified	Propionic acidemia	26163321	details
Urine	Detected and Quantified	566-704 umol/mmol creatinine	Children (1-13 years old)	Female	3-Hydroxyisobutyryl-coa hydrolase deficiency	26163321	details
Urine	Detected and Quantified	638 umol/mmol creatinine	Not Specified	Not Specified	Cobalamin A disease	26163321	details
Urine	Detected and Quantified	33 umol/mmol creatinine	Not Specified	Not Specified	Cobalamin C disease	26163321	details

Associated Disorders and Diseases

Disease References

Metastatic melanoma
Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, Koh AY: Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients. Neoplasia. 2017 Oct;19(10):848-855. doi: 10.1016/j.neo.2017.08.004. Epub 2017 Sep 15. [PubMed:28923537 ]
Colorectal cancer
Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Attachment loss
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Missing teeth
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Periodontal Probing Depth
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Methylmalonyl-CoA mutase deficiency
Peters H, Ferdinandusse S, Ruiter JP, Wanders RJ, Boneh A, Pitt J: Metabolite studies in HIBCH and ECHS1 defects: Implications for screening. Mol Genet Metab. 2015 Aug;115(4):168-73. doi: 10.1016/j.ymgme.2015.06.008. Epub 2015 Jun 24. [PubMed:26163321 ]
3-Hydroxyisobutyryl-coa hydrolase deficiency
Peters H, Ferdinandusse S, Ruiter JP, Wanders RJ, Boneh A, Pitt J: Metabolite studies in HIBCH and ECHS1 defects: Implications for screening. Mol Genet Metab. 2015 Aug;115(4):168-73. doi: 10.1016/j.ymgme.2015.06.008. Epub 2015 Jun 24. [PubMed:26163321 ]
Cobalamin A disease
Peters H, Ferdinandusse S, Ruiter JP, Wanders RJ, Boneh A, Pitt J: Metabolite studies in HIBCH and ECHS1 defects: Implications for screening. Mol Genet Metab. 2015 Aug;115(4):168-73. doi: 10.1016/j.ymgme.2015.06.008. Epub 2015 Jun 24. [PubMed:26163321 ]
Methylmalonic aciduria and homocystinuria, cblC type
Peters H, Ferdinandusse S, Ruiter JP, Wanders RJ, Boneh A, Pitt J: Metabolite studies in HIBCH and ECHS1 defects: Implications for screening. Mol Genet Metab. 2015 Aug;115(4):168-73. doi: 10.1016/j.ymgme.2015.06.008. Epub 2015 Jun 24. [PubMed:26163321 ]

Associated OMIM IDs

114500 (Colorectal cancer)
250620 (3-Hydroxyisobutyryl-coa hydrolase deficiency)
277400 (Methylmalonic aciduria and homocystinuria, cblC type)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028799

KNApSAcK ID

Not Available

Chemspider ID

389255

KEGG Compound ID

C04272

BioCyc ID

DIOH-ISOVALERATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440279

PDB ID

Not Available

ChEBI ID

15684

Food Biomarker Ontology

Not Available

VMH ID

23DHMB

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for (R)-2,3-Dihydroxy-isovalerate (HMDB0012141)

Structure for HMDB0012141 ((R)-2,3-Dihydroxy-isovalerate)