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Showing metabocard for 2-Hydroxy-3-methylbutyric acid (HMDB0000407)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:48 UTC
HMDB IDHMDB0000407
Secondary Accession Numbers
  • HMDB00407
  • HMDB0062584
  • HMDB62584
Metabolite Identification
Common Name2-Hydroxy-3-methylbutyric acid
Description2-Hydroxy-3-methylbutyric acid (also known as 2-hydroxyisovaleric acid) is a metabolite found in the urine of patients with phenylketonuria (PMID: 7978272 ), methylmalonic acidemia, propionic acidemia, 3-ketothiolase deficiency, isovaleric acidemia, 3-methylcrotonylglycemia, 3-hydroxy-3-methylglutaric acidemia, multiple carboxylase deficiency, glutaric aciduria, ornithine transcarbamylase deficiency, glyceroluria, tyrosinemia type I, galactosemia, and maple syrup urine disease (PMID: 11048741 ). 2-Hydroxyisovaleric acid has also been identified in the urine of patients with lactic acidosis and ketoacidosis (PMID: 884872 ), and in the urine of severely asphyxiated babies (PMID: 1610944 ). 2-Hydroxyisovaleric acid originates mainly from ketogenesis and from the metabolism of valine, leucine, and isoleucine (PMID: 6434570 ). 2-Hydroxy-3-methylbutyric acid has been identified in the human placenta (PMID: 32033212 ).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000407 (2-Hydroxy-3-methylbutyric acid)

  Mrv1652303062019112D          

  8  7  0  0  0  0            999 V2000
10007.706010007.5050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10008.421410007.9171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10009.134810007.5050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10008.421410008.7418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.991310007.9171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.276510007.5050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10006.991310008.7418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10007.706010006.6797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
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3D MOL for HMDB0000407 (2-Hydroxy-3-methylbutyric acid)

HMDB0000407
     RDKit          3D
2-Hydroxy-3-methylbutyric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.2200    1.3793    0.5501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5049    0.0437    0.4608 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3826   -0.9209   -0.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8249    0.2804   -0.2061 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6409    0.8060   -1.4813 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6530   -0.9190   -0.3144 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0985   -1.3581   -1.4053 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9810   -1.6316    0.8322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5580    2.0536    1.1224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1933    1.2301    1.0977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3931    1.8100   -0.4408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3613   -0.3007    1.5051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0413   -0.4230   -1.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0794   -1.4223    0.4691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8179   -1.7268   -0.7803 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3476    1.0629    0.3900 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0305    1.6967   -1.5946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9753   -1.6601    1.0645 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  8 18  1  0
M  END
Download

3D SDF for HMDB0000407 (2-Hydroxy-3-methylbutyric acid)

  Mrv1652303062019112D          

  8  7  0  0  0  0            999 V2000
10007.706010007.5050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10008.421410007.9171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10009.134810007.5050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10008.421410008.7418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.991310007.9171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.276510007.5050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10006.991310008.7418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10007.706010006.6797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000407

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)C(O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O3/c1-3(2)4(6)5(7)8/h3-4,6H,1-2H3,(H,7,8)

> <INCHI_KEY>
NGEWQZIDQIYUNV-UHFFFAOYSA-N

> <FORMULA>
C5H10O3

> <MOLECULAR_WEIGHT>
118.1311

> <EXACT_MASS>
118.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
11.76765686162724

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-3-methylbutanoic acid

> <ALOGPS_LOGP>
0.10

> <JCHEM_LOGP>
0.4156657033333334

> <ALOGPS_LOGS>
0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.053181861607996

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.138361788089717

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8921886131871277

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
27.8354

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.15e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxyisovaleric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000407 (2-Hydroxy-3-methylbutyric acid)

HMDB0000407
     RDKit          3D
2-Hydroxy-3-methylbutyric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.2200    1.3793    0.5501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5049    0.0437    0.4608 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3826   -0.9209   -0.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8249    0.2804   -0.2061 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6409    0.8060   -1.4813 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6530   -0.9190   -0.3144 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0985   -1.3581   -1.4053 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9810   -1.6316    0.8322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5580    2.0536    1.1224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1933    1.2301    1.0977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3931    1.8100   -0.4408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3613   -0.3007    1.5051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0413   -0.4230   -1.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0794   -1.4223    0.4691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8179   -1.7268   -0.7803 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3476    1.0629    0.3900 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0305    1.6967   -1.5946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9753   -1.6601    1.0645 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  8 18  1  0
M  END
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PDB for HMDB0000407 (2-Hydroxy-3-methylbutyric acid)

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  C   UNK     0    8681.0518680.676   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8682.3878681.445   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8683.7188680.676   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8682.3878682.985   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8679.7178681.445   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8678.3838680.676   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8679.7178682.985   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8681.0518679.135   0.000  0.00  0.00           O+0
CONECT    1    2    5    8                                                  
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    1                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0000407 (2-Hydroxy-3-methylbutyric acid)

COMPND    HMDB0000407
HETATM    1  C1  UNL     1      -1.220   1.379   0.550  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.505   0.044   0.461  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.383  -0.921  -0.265  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.825   0.280  -0.206  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.641   0.806  -1.481  1.00  0.00           O  
HETATM    6  C5  UNL     1       1.653  -0.919  -0.314  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.099  -1.358  -1.405  1.00  0.00           O  
HETATM    8  O3  UNL     1       1.981  -1.632   0.832  1.00  0.00           O  
HETATM    9  H1  UNL     1      -0.558   2.054   1.122  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.193   1.230   1.098  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.393   1.810  -0.441  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.361  -0.301   1.505  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.041  -0.423  -1.004  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.079  -1.422   0.469  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.818  -1.727  -0.780  1.00  0.00           H  
HETATM   16  H8  UNL     1       1.348   1.063   0.390  1.00  0.00           H  
HETATM   17  H9  UNL     1       1.031   1.697  -1.595  1.00  0.00           H  
HETATM   18  H10 UNL     1       2.975  -1.660   1.065  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    4   12
CONECT    3   13   14   15
CONECT    4    5    6   16
CONECT    5   17
CONECT    6    7    7    8
CONECT    8   18
END
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SMILES for HMDB0000407 (2-Hydroxy-3-methylbutyric acid)

CC(C)C(O)C(O)=O
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INCHI for HMDB0000407 (2-Hydroxy-3-methylbutyric acid)

InChI=1S/C5H10O3/c1-3(2)4(6)5(7)8/h3-4,6H,1-2H3,(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC5H10O3
Average Molecular Weight118.1311
Monoisotopic Molecular Weight118.062994186
IUPAC Name2-hydroxy-3-methylbutanoic acid
Traditional Name2-hydroxyisovaleric acid
CAS Registry Number4026-18-0
SMILES
CC(C)C(O)C(O)=O
InChI Identifier
InChI=1S/C5H10O3/c1-3(2)4(6)5(7)8/h3-4,6H,1-2H3,(H,7,8)
InChI KeyNGEWQZIDQIYUNV-UHFFFAOYSA-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Branched fatty acid
  • Hydroxy fatty acid
  • Methyl-branched fatty acid
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility350 mg/mLNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg118.64930932474
[M-H]-Not Available118.649http://allccs.zhulab.cn/database/detail?ID=AllCCS00000192
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Pregnancy
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: Metabolomic analysis for first-trimester Down syndrome prediction. Am J Obstet Gynecol. 2013 May;208(5):371.e1-8. doi: 10.1016/j.ajog.2012.12.035. Epub 2013 Jan 8. [PubMed:23313728 ]
Maple syrup urine disease
  1. Shigematsu Y, Kikuchi K, Momoi T, Sudo M, Kikawa Y, Nosaka K, Kuriyama M, Haruki S, Sanada K, Hamano N, et al.: Organic acids and branched-chain amino acids in body fluids before and after multiple exchange transfusions in maple syrup urine disease. J Inherit Metab Dis. 1983;6(4):183-9. [PubMed:6422161 ]
  2. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. 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 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Dihydrolipoamide Dehydrogenase Deficiency
  1. Kuhara T, Shinka T, Inoue Y, Matsumoto M, Yoshino M, Sakaguchi Y, Matsumoto I: Studies of urinary organic acid profiles of a patient with dihydrolipoyl dehydrogenase deficiency. Clin Chim Acta. 1983 Sep 30;133(2):133-40. [PubMed:6688766 ]
Associated OMIM IDs
  • 248600 (Maple syrup urine disease)
  • 114500 (Colorectal cancer)
  • 610247 (Eosinophilic esophagitis)
  • 246900 (Dihydrolipoamide Dehydrogenase Deficiency)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022023
KNApSAcK IDNot Available
Chemspider ID90190
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5396
PubChem Compound99823
PDB IDNot Available
ChEBI ID60645
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000158
Good Scents IDNot Available
References
Synthesis ReferencePerekalin, V. V.; Petryaeva, A. K.; Zobacheva, M. M.; Metelkina, E. L. A new method of synthesis of a-hydroxy and a-oxo acids. Doklady Akademii Nauk SSSR (1966), 166(5), 1129-31.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Sulfotransferase family cytosolic 2B member 1
General function:
Involved in sulfotransferase activity
Specific function:
Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs and xenobiotic compounds. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Sulfates hydroxysteroids like DHEA. Isoform 1 preferentially sulfonates cholesterol, and isoform 2 avidly sulfonates pregnenolone but not cholesterol.
Gene Name:
SULT2B1
Uniprot ID:
O00204
Molecular weight:
39598.595
Reactions
2-Hydroxy-3-methylbutyric acid → 3-methyl-2-(sulfooxy)butanoic aciddetails
Enzyme Details
2. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
2-Hydroxy-3-methylbutyric acid → 6-(1-carboxy-2-methylpropoxy)-3,4,5-trihydroxyoxane-2-carboxylic aciddetails
2-Hydroxy-3-methylbutyric acid → 3,4,5-trihydroxy-6-[(2-hydroxy-3-methylbutanoyl)oxy]oxane-2-carboxylic aciddetails