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Showing NP-Card for 2-Methyl-3-hydroxybutyric acid (NP0083431)

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Record Information
Version2.0
Created at2022-04-29 04:28:52 UTC
Updated at2022-04-29 04:28:52 UTC
NP-MRD IDNP0083431
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Methyl-3-hydroxybutyric acid
Description2-Methyl-3-hydroxybutyric acid, also known as 3-hydroxy-2-methylbutyric acid or 2-methyl-3-hydroxybutanoate, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. Differences in the enantiomeric ratio of HMBA may originate from the enantioselectivity of different enzyme systems (PMID 10755375 ). 2-Methyl-3-hydroxybutyric acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 2-Methyl-3-hydroxybutyric acid is a potentially toxic compound. 2-Methyl-3-hydroxybutyric acid is found in Homo sapiens (Urine). 2-Methyl-3-hydroxybutyric acid was first documented in 1975 (PMID: 126826). 2-Methyl-3-hydroxybutyric acid, with regard to humans, has been found to be associated with several diseases such as ketosis and 2-methyl-3-hydroxybutyryl-coa dehydrogenase deficiency; 2-methyl-3-hydroxybutyric acid has also been linked to several inborn metabolic disorders including beta-ketothiolase deficiency and propionic acidemia (PMID: 6467607) (PMID: 10755375) (PMID: 12872843).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0083431 (2-Methyl-3-hydroxybutyric acid)

2-Methyl-3-hydroxybutyric acid.mol
  Mrv0541 02231218282D          

  8  7  0  0  0  0            999 V2000
    0.7137   -0.2069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.2069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7152   -0.2043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.2095    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7122   -1.0319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.2043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7167   -1.0293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0015    1.0319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
  3  7  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
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3D MOL for NP0083431 (2-Methyl-3-hydroxybutyric acid)

     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.4434   -1.4576    0.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5349   -0.2976    0.2886 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1977    0.9610   -0.0684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3021    0.9125   -0.6666 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6668    2.2101    0.2209 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8264   -0.4487   -0.3455 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6325    0.7656   -0.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4466   -1.5476    0.2382 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9987   -1.2394   -0.9135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1611   -1.5052    0.9045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9267   -2.4270   -0.0169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3492   -0.2576    1.3993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6121    2.8808   -0.5221 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7729   -0.5529   -1.4472 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7052    0.4765    0.0309 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3626    1.2015    0.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5728    1.5627   -0.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8736   -1.2370    1.0692 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  8  1  0
  6  2  1  0
  2  1  1  0
  2  3  1  0
  3  5  1  0
  3  4  2  0
  7 15  1  0
  7 16  1  0
  7 17  1  0
  6 14  1  6
  8 18  1  0
  2 12  1  1
  1  9  1  0
  1 10  1  0
  1 11  1  0
  5 13  1  0
M  END
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3D SDF for NP0083431 (2-Methyl-3-hydroxybutyric acid)

2-Methyl-3-hydroxybutyric acid.mol
  Mrv0541 02231218282D          

  8  7  0  0  0  0            999 V2000
    0.7137   -0.2069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.2069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7152   -0.2043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.2095    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7122   -1.0319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.2043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7167   -1.0293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0015    1.0319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
  3  7  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0083431

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
VEXDRERIMPLZLU-UHFFFAOYSA-N

> <FORMULA>
C5H10O3

> <MOLECULAR_WEIGHT>
118.1311

> <EXACT_MASS>
118.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.829094147373619

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.13

> <JCHEM_LOGP>
0.1559802790000001

> <ALOGPS_LOGS>
0.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.303379950745505

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.513689206767185

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7866129389831196

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
28.038600000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.36e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nilic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0083431 (2-Methyl-3-hydroxybutyric acid)

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PDB for NP0083431 (2-Methyl-3-hydroxybutyric acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 2-Methyl-3-hydroxybutyric acid.mol                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       1.332  -0.386   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.386   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.335  -0.381   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667   0.391   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.329  -1.926   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       2.667   0.381   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -1.338  -1.921   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.003   1.926   0.000  0.00  0.00           C+0
CONECT    1    2    5    6                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3                                                            
CONECT    5    1                                                            
CONECT    6    1                                                            
CONECT    7    3                                                            
CONECT    8    2                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0083431 (2-Methyl-3-hydroxybutyric acid)
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SMILES for NP0083431 (2-Methyl-3-hydroxybutyric acid)
CC(O)C(C)C(O)=O
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INCHI for NP0083431 (2-Methyl-3-hydroxybutyric acid)
InChI=1S/C5H10O3/c1-3(4(2)6)5(7)8/h3-4,6H,1-2H3,(H,7,8)
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View in JSmol
Synonyms
ValueSource
2-Methyl-3-hydroxybutanoic acidChEBI
3-Hydroxy-2-methylbutyric acidChEBI
2-Methyl-3-hydroxybutanoateGenerator
3-Hydroxy-2-methylbutyrateGenerator
2-Methyl-3-hydroxybutyrateGenerator
3-Hydroxy-2-methyl-butyrateHMDB
3-Hydroxy-2-methyl-butyric acidHMDB
3-Hydroxy-2-methylbutanoateHMDB
3-Hydroxy-2-methylbutanoic acidHMDB
a-Methyl-b-hydroxybutyrateHMDB
a-Methyl-b-hydroxybutyric acidHMDB
alpha-Methyl-beta-hydroxybutyrateHMDB
alpha-Methyl-beta-hydroxybutyric acidHMDB
NilateHMDB
Nilic acidHMDB
2-Methyl-3-hydroxybutyric acid, (R-(r*,s*))-isomerHMDB
Chemical FormulaC5H10O3
Average Mass118.1311 Da
Monoisotopic Mass118.06299 Da
IUPAC Name3-hydroxy-2-methylbutanoic acid
Traditional Namenilic acid
CAS Registry NumberNot Available
SMILES
CC(O)C(C)C(O)=O
InChI Identifier
InChI=1S/C5H10O3/c1-3(4(2)6)5(7)8/h3-4,6H,1-2H3,(H,7,8)
InChI KeyVEXDRERIMPLZLU-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Homo sapiens (Urine)Animalia
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
  • Beta-hydroxy acid
    • 

  • Branched fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Methyl-branched fatty acid
    • 

  • Hydroxy acid
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.13ALOGPS
logP0.16ChemAxon
logS0.45ALOGPS
pKa (Strongest Acidic)4.51ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity28.04 m³·mol⁻¹ChemAxon
Polarizability11.83 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000354  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021977  
KNApSAcK IDNot Available
Chemspider ID141015  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID3786  
PubChem Compound160471  
PDB IDNot Available
ChEBI ID37051  
Good Scents IDNot Available
References
General References
  1. Landaas S: Accumulation of 3-hydroxyisobutyric acid, 2-methyl-3-hydroxybutyric acid and 3-hydroxyisovaleric acid in ketoacidosis. Clin Chim Acta. 1975 Oct 15;64(2):143-54. [PubMed:126826  ] 
  2. Jakobs C, Sweetman L, Nyhan WL: Hydroxy acid metabolites of branched-chain amino acids in amniotic fluid. Clin Chim Acta. 1984 Jul 16;140(2):157-66. [PubMed:6467607  ] 
  3. Heil M, Podebrad F, Prado E, Beck T, Mosand A, Sewell AC, Bohles H, Lehnert W: Enantioselective analysis of ketone bodies in patients with beta-ketothiolase deficiency, medium-chain acyl coenzyme A dehydrogenase deficiency and ketonemic vomiting. J Chromatogr B Biomed Sci Appl. 2000 Mar 10;739(2):313-24. [PubMed:10755375  ] 
  4. Sutton VR, O'Brien WE, Clark GD, Kim J, Wanders RJ: 3-Hydroxy-2-methylbutyryl-CoA dehydrogenase deficiency. J Inherit Metab Dis. 2003;26(1):69-71. doi: 10.1023/a:1024083715568. [PubMed:12872843  ]