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Showing metabocard for (R)-3-Hydroxyisobutyric acid (HMDB0000336)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:55:55 UTC
HMDB IDHMDB0000336
Secondary Accession Numbers
  • HMDB00336
Metabolite Identification
Common Name(R)-3-Hydroxyisobutyric acid
Description(R)-3-Hydroxyisobutyric acid (3-HIBA) is an organic acid. The chiral metabolites 3-hydroxyisobutyric acid (HIBA) and 3-aminoisobutyric acid (AIBA) are intermediates in the pathways of L-valine and thymine and play 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 ) (PMID: 10686279 ). (R)-3-Hydroxyisobutyric acid has been identified in the human placenta (PMID: 32033212 ).
Structure
Data?1582752124
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000336 ((R)-3-Hydroxyisobutyric acid)

  Mrv1652307101917012D          

  7  6  0  0  1  0            999 V2000
   18.9558   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0981   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8124   -2.9330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5268   -4.1704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.2413   -3.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5268   -4.9954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8124   -3.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  7  1  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  1  0  0  0
  4  7  1  0  0  0  0
M  END
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3D MOL for HMDB0000336 ((R)-3-Hydroxyisobutyric acid)

HMDB0000336
     RDKit          3D
(R)-3-Hydroxyisobutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
    0.3802    1.5829    0.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2283    0.1864   -0.4860 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2372   -0.2358   -0.3864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5671   -0.1965    0.9586 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0044   -0.7387    0.3683 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6514   -0.3339    1.3708 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0443   -2.1164    0.0836 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4103    1.9279   -0.1327 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2171    1.5638    1.1553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3086    2.3115   -0.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5463    0.1549   -1.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8364    0.5362   -0.9230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3684   -1.2241   -0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9172   -1.0332    1.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7525   -2.3850   -0.6026 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  6
  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 HMDB0000336 ((R)-3-Hydroxyisobutyric acid)

  Mrv1652307101917012D          

  7  6  0  0  1  0            999 V2000
   18.9558   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0981   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8124   -2.9330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5268   -4.1704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.2413   -3.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5268   -4.9954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8124   -3.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  7  1  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  1  0  0  0
  4  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000336

> <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-/m1/s1

> <INCHI_KEY>
DBXBTMSZEOQQDU-GSVOUGTGSA-N

> <FORMULA>
C4H8O3

> <MOLECULAR_WEIGHT>
104.1045

> <EXACT_MASS>
104.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
9.982094489313155

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-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>
(R)-3-hydroxyisobutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000336 ((R)-3-Hydroxyisobutyric acid)

HMDB0000336
     RDKit          3D
(R)-3-Hydroxyisobutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
    0.3802    1.5829    0.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2283    0.1864   -0.4860 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2372   -0.2358   -0.3864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5671   -0.1965    0.9586 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0044   -0.7387    0.3683 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6514   -0.3339    1.3708 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0443   -2.1164    0.0836 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4103    1.9279   -0.1327 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2171    1.5638    1.1553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3086    2.3115   -0.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5463    0.1549   -1.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8364    0.5362   -0.9230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3684   -1.2241   -0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9172   -1.0332    1.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7525   -2.3850   -0.6026 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  6
  3 12  1  0
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0000336 ((R)-3-Hydroxyisobutyric acid)

HEADER    PROTEIN                                 10-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-JUL-19         0                                  
HETATM    1  O   UNK     0      35.384  -7.785   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.050  -7.785   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      31.383  -5.475   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      32.717  -7.785   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      34.050  -7.015   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      32.717  -9.325   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      31.383  -7.015   0.000  0.00  0.00           C+0
CONECT    1    5                                                            
CONECT    2    7                                                            
CONECT    3    7                                                            
CONECT    4    5    6    7                                                  
CONECT    5    1    4                                                       
CONECT    6    4                                                            
CONECT    7    2    3    4                                                  
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0000336 ((R)-3-Hydroxyisobutyric acid)

COMPND    HMDB0000336
HETATM    1  C1  UNL     1       0.380   1.583   0.071  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.228   0.186  -0.486  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.237  -0.236  -0.386  1.00  0.00           C  
HETATM    4  O1  UNL     1      -1.567  -0.196   0.959  1.00  0.00           O  
HETATM    5  C4  UNL     1       1.004  -0.739   0.368  1.00  0.00           C  
HETATM    6  O2  UNL     1       1.651  -0.334   1.371  1.00  0.00           O  
HETATM    7  O3  UNL     1       1.044  -2.116   0.084  1.00  0.00           O  
HETATM    8  H1  UNL     1       1.410   1.928  -0.133  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.217   1.564   1.155  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.309   2.311  -0.404  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.546   0.155  -1.539  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.836   0.536  -0.923  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.368  -1.224  -0.849  1.00  0.00           H  
HETATM   14  H7  UNL     1      -1.917  -1.033   1.315  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.752  -2.385  -0.603  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 HMDB0000336 ((R)-3-Hydroxyisobutyric acid)

C[C@H](CO)C(O)=O
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INCHI for HMDB0000336 ((R)-3-Hydroxyisobutyric acid)

InChI=1S/C4H8O3/c1-3(2-5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC4H8O3
Average Molecular Weight104.1045
Monoisotopic Molecular Weight104.047344122
IUPAC Name(2R)-3-hydroxy-2-methylpropanoic acid
Traditional Name(R)-3-hydroxyisobutyric acid
CAS Registry Number1910-47-0
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-/m1/s1
InChI KeyDBXBTMSZEOQQDU-GSVOUGTGSA-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
ProcessNot Available
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 LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified21.0 +/- 2.0 uMAdult (>18 years old)Both
Normal		 details
Cerebrospinal Fluid (CSF)Detected and Quantified6 +/- 3 uMAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified<95 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
 details
UrineDetected and Quantified12.33 (5.09-23.56) umol/mmol creatinineNewborn (0-30 days old)Both
Normal
    • Analysis of 40 NI...
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified38.0 +/- 5.0 uMAdult (>18 years old)Both
Diabetes 		details
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 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021960
KNApSAcK IDNot Available
Chemspider ID9392288
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11217234
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000146
Good Scents IDNot Available
References
Synthesis ReferenceSprecher, M.; Sprinson, David B. Preparation of (R)-b-hydroxyisobutyric acid from threo-3-methyl-L-aspartate. Journal of Biological Chemistry (1966), 241(4), 868-71.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Podebrad F, Heil M, Beck T, Mosandl A, Sewell AC, Bohles H: Stereodifferentiation of 3-hydroxyisobutyric- and 3-aminoisobutyric acid in human urine by enantioselective multidimensional capillary gas chromatography-mass spectrometry. Clin Chim Acta. 2000 Feb 25;292(1-2):93-105. [PubMed:10686279 ]
  2. Gray RG, Pollitt RJ, Webley J: Methylmalonic semialdehyde dehydrogenase deficiency: demonstration of defective valine and beta-alanine metabolism and reduced malonic semialdehyde dehydrogenase activity in cultured fibroblasts. Biochem Med Metab Biol. 1987 Aug;38(1):121-4. [PubMed:3117077 ]
  3. Roe CR, Struys E, Kok RM, Roe DS, Harris RA, Jakobs C: Methylmalonic semialdehyde dehydrogenase deficiency: psychomotor delay and methylmalonic aciduria without metabolic decompensation. Mol Genet Metab. 1998 Sep;65(1):35-43. [PubMed:9787093 ]
  4. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]