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Showing NP-Card for 2-Hydroxy-3-methylbutyric acid (NP0000537)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2024-09-03 04:17:09 UTC
NP-MRD IDNP0000537
Natural Product DOIhttps://doi.org/10.57994/0937
Secondary Accession NumbersNone
Natural Product 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 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000537 (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
Download

3D MOL for NP0000537 (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 NP0000537 (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>
NP0000537

> <DATABASE_NAME>
NP-MRD

> <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 NP0000537 (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

PDB for NP0000537 (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 NP0000537 (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 NP0000537 (2-Hydroxy-3-methylbutyric acid)

CC(C)C(O)C(O)=O
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INCHI for NP0000537 (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 JSmol
Synonyms
ValueSource
2-Hydroxyisopentanoic acidChEBI
2-Hydroxyisovaleric acidChEBI
3-Methyl-2-hydroxybutyric acidChEBI
alpha-Hydroxyisovaleric acidChEBI
2-HydroxyisopentanoateGenerator
2-HydroxyisovalerateGenerator
3-Methyl-2-hydroxybutyrateGenerator
a-HydroxyisovalerateGenerator
a-Hydroxyisovaleric acidGenerator
alpha-HydroxyisovalerateGenerator
Α-hydroxyisovalerateGenerator
Α-hydroxyisovaleric acidGenerator
2-Hydroxy-3-methylbutyrateGenerator
2-Hydroxy-3-methyl-butyric acidHMDB
2-Hydroxy-3-methylbutanoateHMDB
2-Hydroxy-3-methylbutanoic acidHMDB
2-OxyisovalerateHMDB
2-Oxyisovaleric acidHMDB
DL-2-Hydroxy-3-methylbutanoateHMDB
DL-2-Hydroxy-3-methylbutanoic acidHMDB
DL-2-HydroxyisovalerateHMDB
DL-2-Hydroxyisovaleric acidHMDB
DL-a-HydroxyisovalerateHMDB
DL-a-Hydroxyisovaleric acidHMDB
DL-alpha-HydroxyisovalerateHMDB
DL-alpha-Hydroxyisovaleric acidHMDB
2-Hydroxyisovaleric acid, monosodium salt, (S)-isomerHMDB
2-Hydroxyisovaleric acid, (S)-isomerHMDB
2-Hydroxyisovaleric acid, calcium (2:1) saltHMDB
2-Hydroxyisovaleric acid, (R)-isomerHMDB
Chemical FormulaC5H10O3
Average Mass118.1311 Da
Monoisotopic Mass118.06299 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D_DEPT NMR13C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-09View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2023-09-19View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2023-09-19View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2023-09-19View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2023-09-19View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2023-09-19View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600, CD3OD, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-09View Spectrum
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
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Streptomyces cavourensisLOTUS Database
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
  • 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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point237.00 to 238.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility350 mg/mLNot Available
LogP0.013 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility215 g/LALOGPS
logP0.1ALOGPS
logP0.42ChemAxon
logS0.26ALOGPS
pKa (Strongest Acidic)4.14ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity27.84 m³·mol⁻¹ChemAxon
Polarizability11.77 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000407
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDrw1505951
References
General References
  1. Bergstrom T, Greter J, Levin AH, Steen G, Tryding N, Wass U: Propionyl-CoA carboxylase deficiency: case report, effect of low-protein diet and identification of 3-oxo-2-methylvaleric acid 3-hydroxy-2-methylvaleric acid, and maleic acid in urine. Scand J Clin Lab Invest. 1981 Apr;41(2):117-26. [PubMed:7313494 ]
  2. Landaas S, Jakobs C: The occurrence of 2-hydroxyisovaleric acid in patients with lactic acidosis and ketoacidosis. Clin Chim Acta. 1977 Aug 1;78(3):489-93. [PubMed:884872 ]
  3. Liebich HM, Forst C: Hydroxycarboxylic and oxocarboxylic acids in urine: products from branched-chain amino acid degradation and from ketogenesis. J Chromatogr. 1984 Aug 10;309(2):225-42. [PubMed:6434570 ]
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