Showing metabocard for 2-Hydroxy-3-methylbutyric acid (MMDBc0000515)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:31 UTC
Update Date2024-04-30 19:32:44 UTC
Metabolite IDMMDBc0000515
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fd12fcdb9e8>


  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 #<Metabolite:0x00007fd12fcdb9e8>

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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3D SDF for #<Metabolite:0x00007fd12fcdb9e8>


  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>
MMDBc0000515

> <DATABASE_NAME>
MIME

> <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

$$$$
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3D-SDF for #<Metabolite:0x00007fd12fcdb9e8>

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 #<Metabolite:0x00007fd12fcdb9e8>

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 #<Metabolite:0x00007fd12fcdb9e8>

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 #<Metabolite:0x00007fd12fcdb9e8>

CC(C)C(O)C(O)=O
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INCHI for #<Metabolite:0x00007fd12fcdb9e8>

InChI=1S/C5H10O3/c1-3(2)4(6)5(7)8/h3-4,6H,1-2H3,(H,7,8)
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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
Molecular FormulaC5H10O3
Average Mass118.1311
Monoisotopic Mass118.062994186
IUPAC Name2-hydroxy-3-methylbutanoic acid
Traditional Name2-hydroxyisovaleric acid
CAS Registry NumberNot Available
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