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Showing metabocard for (S)-3-Hydroxyisobutyric acid (HMDB0000023)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:27 UTC
HMDB IDHMDB0000023
Secondary Accession Numbers
Metabolite Identification
Common Name(S)-3-Hydroxyisobutyric acid
Description(S)-3-Hydroxyisobutyric acid (3-HIBA) (CAS: 2068-83-9) is an organic acid. 3-HIBA is an intermediate in L-valine metabolism. 3-HIBA plays an important role in the diagnosis of the very rare inherited metabolic diseases 3-hydroxyisobutyric aciduria (OMIM: 236795 ) and methylmalonic semialdehyde dehydrogenase deficiency (OMIM: 603178 ). Patients with 3-hydroxyisobutyric aciduria excrete a significant amount of 3-HIBA not only during the acute stage but also when stable. 3-Hydroxyisobutyric aciduria is caused by a 3-hydroxyisobutyryl-CoA dehydrogenase deficiency (PMID: 18329219 ). The severity of this disease varies from case to case. Most patients exhibit dysmorphic features, such as a small triangular face, a long philtrum, low set ears, and micrognathia (PMID: 10686279 ). Lactic acidemia is also found in the affected patients, indicating that mitochondrial dysfunction is involved. 3-HIBA appears to specifically inhibit the function of the respiratory chain complex I-III and mitochondrial creatine kinase (PMID: 18329219 ). BioTransformer predicts that 3-HIBA is a product of 2-methylpropanoic acid metabolism via a hydroxylation-of-terminal-methyl reaction catalyzed by CYP2B6 and CYP2E1 enzymes (PMID: 30612223 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000023 ((S)-3-Hydroxyisobutyric acid)

  Mrv1652306242019402D          

  7  6  0  0  0  0            999 V2000
10000.0234 9999.7990    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.308710000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.738110000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0234 9998.9737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5940 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.308710001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.4559 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000023 ((S)-3-Hydroxyisobutyric acid)

HMDB0000023
     RDKit          3D
(S)-3-Hydroxyisobutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -0.3559    1.5180   -0.1100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1376    0.1493    0.4689 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5975   -0.9442   -0.4933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -0.8334   -0.7899 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2954   -0.1161    0.7590 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7216   -0.3782    1.9012 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774   -0.0639   -0.3055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4134    1.8228    0.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2562    2.2420    0.4585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0858    1.5442   -1.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7353   -0.0027    1.3962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4138   -1.9142   -0.0006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0286   -0.8901   -1.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4576   -1.2771   -0.0536 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7232   -0.8564   -0.6167 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  1
  3 12  1  0
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0000023 ((S)-3-Hydroxyisobutyric acid)

  Mrv1652306242019402D          

  7  6  0  0  0  0            999 V2000
10000.0234 9999.7990    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.308710000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.738110000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0234 9998.9737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5940 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.308710001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.4559 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000023

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@@H](CO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O3/c1-3(2-5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m0/s1

> <INCHI_KEY>
DBXBTMSZEOQQDU-VKHMYHEASA-N

> <FORMULA>
C4H8O3

> <MOLECULAR_WEIGHT>
104.1045

> <EXACT_MASS>
104.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
9.981369504774722

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-3-hydroxy-2-methylpropanoic acid

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
-0.26059474566666674

> <ALOGPS_LOGS>
0.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.518589741896943

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.365338407814565

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6927927583619056

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
23.6198

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.71e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-3-hydroxyisobutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000023 ((S)-3-Hydroxyisobutyric acid)

HMDB0000023
     RDKit          3D
(S)-3-Hydroxyisobutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -0.3559    1.5180   -0.1100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1376    0.1493    0.4689 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5975   -0.9442   -0.4933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9484   -0.8334   -0.7899 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2954   -0.1161    0.7590 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7216   -0.3782    1.9012 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774   -0.0639   -0.3055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4134    1.8228    0.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2562    2.2420    0.4585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0858    1.5442   -1.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7353   -0.0027    1.3962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4138   -1.9142   -0.0006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0286   -0.8901   -1.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4576   -1.2771   -0.0536 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7232   -0.8564   -0.6167 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  1
  3 12  1  0
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0000023 ((S)-3-Hydroxyisobutyric acid)

HEADER    PROTEIN                                 24-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-20         0                                  
HETATM    1  C   UNK     0    8666.7108666.291   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8665.3768667.061   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8668.0448667.061   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8666.7108664.751   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8664.0428666.291   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8665.3768668.601   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8669.3848666.291   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1                                                            
CONECT    5    2                                                            
CONECT    6    2                                                            
CONECT    7    3                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0000023 ((S)-3-Hydroxyisobutyric acid)

COMPND    HMDB0000023
HETATM    1  C1  UNL     1      -0.356   1.518  -0.110  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.138   0.149   0.469  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.598  -0.944  -0.493  1.00  0.00           C  
HETATM    4  O1  UNL     1      -1.948  -0.833  -0.790  1.00  0.00           O  
HETATM    5  C4  UNL     1       1.295  -0.116   0.759  1.00  0.00           C  
HETATM    6  O2  UNL     1       1.722  -0.378   1.901  1.00  0.00           O  
HETATM    7  O3  UNL     1       2.177  -0.064  -0.305  1.00  0.00           O  
HETATM    8  H1  UNL     1      -1.413   1.823   0.011  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.256   2.242   0.458  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.086   1.544  -1.171  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.735  -0.003   1.396  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.414  -1.914  -0.001  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.029  -0.890  -1.454  1.00  0.00           H  
HETATM   14  H7  UNL     1      -2.458  -1.277  -0.054  1.00  0.00           H  
HETATM   15  H8  UNL     1       2.723  -0.856  -0.617  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    5   11
CONECT    3    4   12   13
CONECT    4   14
CONECT    5    6    6    7
CONECT    7   15
END
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SMILES for HMDB0000023 ((S)-3-Hydroxyisobutyric acid)

C[C@@H](CO)C(O)=O
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INCHI for HMDB0000023 ((S)-3-Hydroxyisobutyric acid)

InChI=1S/C4H8O3/c1-3(2-5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC4H8O3
Average Molecular Weight104.1045
Monoisotopic Molecular Weight104.047344122
IUPAC Name(2S)-3-hydroxy-2-methylpropanoic acid
Traditional Name(S)-3-hydroxyisobutyric acid
CAS Registry Number26543-05-5
SMILES
C[C@@H](CO)C(O)=O
InChI Identifier
InChI=1S/C4H8O3/c1-3(2-5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m0/s1
InChI KeyDBXBTMSZEOQQDU-VKHMYHEASA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassBeta hydroxy acids and derivatives
Direct ParentBeta hydroxy acids and derivatives
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Diabetes mellitus type 2
  1. Avogaro A, Bier DM: Contribution of 3-hydroxyisobutyrate to the measurement of 3-hydroxybutyrate in human plasma: comparison of enzymatic and gas-liquid chromatography-mass spectrometry assays in normal and in diabetic subjects. J Lipid Res. 1989 Nov;30(11):1811-7. [PubMed:2614280 ]
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  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 ]
3-Hydroxyisobutyric aciduria
  1. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021877
KNApSAcK IDNot Available
Chemspider ID389707
KEGG Compound IDC06001
BioCyc IDCPD-12175
BiGG ID37034
Wikipedia LinkNot Available
METLIN ID483
PubChem Compound440873
PDB IDNot Available
ChEBI ID37373
Food Biomarker OntologyNot Available
VMH ID3HMP
MarkerDB IDMDB00000012
Good Scents IDNot Available
References
Synthesis ReferenceRobison, Robert S.; Doremus, Michael G.L-(+)-b-Hydroxyisobutyric acid by fermentation. U.S. (1986), 5 pp.
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
(S)-3-Hydroxyisobutyric acid → 2-methyl-3-(sulfooxy)propanoic aciddetails
Enzyme Details
2. Peroxisomal bifunctional enzyme
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
EHHADH
Uniprot ID:
Q08426
Molecular weight:
69153.26
Reactions
(S)-3-Hydroxyisobutyric acid + NAD → (S)-Methylmalonic acid semialdehyde + NADH + Hydrogen Iondetails
Enzyme Details
3. Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
General function:
Involved in 3-hydroxyacyl-CoA dehydrogenase activity
Specific function:
Plays an essential role in the mitochondrial beta-oxidation of short chain fatty acids. Exerts it highest activity toward 3-hydroxybutyryl-CoA.
Gene Name:
HADH
Uniprot ID:
Q16836
Molecular weight:
36035.11
Reactions
(S)-3-Hydroxyisobutyric acid + NAD → (S)-Methylmalonic acid semialdehyde + NADH + Hydrogen Iondetails
Enzyme Details
4. 3-hydroxyisobutyrate dehydrogenase, mitochondrial
General function:
Involved in 3-hydroxyisobutyrate dehydrogenase activity
Specific function:
Not Available
Gene Name:
HIBADH
Uniprot ID:
P31937
Molecular weight:
35328.515
Reactions
(S)-3-Hydroxyisobutyric acid + NAD → 2-Methyl-3-oxopropanoic acid + NADHdetails
(S)-3-Hydroxyisobutyric acid + NAD → (S)-Methylmalonic acid semialdehyde + NADH + Hydrogen Iondetails
Enzyme Details
5. 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
(S)-3-Hydroxyisobutyric acid → 6-(2-carboxy-2-methylethoxy)-3,4,5-trihydroxyoxane-2-carboxylic aciddetails
(S)-3-Hydroxyisobutyric acid → 3,4,5-trihydroxy-6-[(3-hydroxy-2-methylpropanoyl)oxy]oxane-2-carboxylic aciddetails
Enzyme Details
6. 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
General function:
Involved in catalytic activity
Specific function:
Hydrolyzes 3-hydroxyisobutyryl-CoA (HIBYL-CoA), a saline catabolite. Has high activity toward isobutyryl-CoA. Could be an isobutyryl-CoA dehydrogenase that functions in valine catabolism. Also hydrolyzes 3-hydroxypropanoyl-CoA.
Gene Name:
HIBCH
Uniprot ID:
Q6NVY1
Molecular weight:
43481.935
Reactions
(S)-3-Hydroxyisobutyryl-CoA + Water → Coenzyme A + (S)-3-Hydroxyisobutyric aciddetails
(S)-3-Hydroxyisobutyryl-CoA + Water → Coenzyme A + (S)-3-Hydroxyisobutyric aciddetails