Showing metabocard for 3-Methylglutaconic acid (MMDBc0000522)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:41 UTC
Update Date2024-04-30 19:32:47 UTC
Metabolite IDMMDBc0000522
Metabolite Identification
Common Name3-Methylglutaconic acid
Description3-Methylglutaconic acid is an intermediate (as the CoA thioester) in the leucine degradative pathway as well as the mevalonate shunt, a pathway that links isoprenoid metabolism with mitochondrial acetyl-CoA metabolism (PMID: 7603789 ). 3-methylglutaconyl-CoA hydratase is involved in the metabolism process of 3-methylglutaconic acid. When present in sufficiently high levels, 3-methylglutaconic acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of 3-methylglutaconic acid are associated with at least five inborn errors of metabolism including 3-hydroxy-3-methylglutaryl-CoA lyase deficiency, 3-methylglutaconic aciduria type I, 3-methylglutaconic aciduria type III, 3-methylglutaconic aciduria type IV, and guanidinoacetate methyltransferase deficiency (GAMT deficiency). 3-Methylglutaconic acid is an organic acid. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart, liver, and kidney abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of the untreated IEMs mentioned above. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92397d98a8>

3-Methylglutaconic acid.mol
  Mrv1652302121822452D          

 10  9  0  0  0  0            999 V2000
    1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  3 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f92397d98a8>

HMDB0000522
     RDKit          3D
3-Methylglutaconic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -0.7065   -1.7463    0.3997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0652   -0.3827    0.2504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9037    0.6154    0.1088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3418    0.4232    0.0966 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9349   -0.6731    0.2149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2046    1.5225   -0.0578 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3977   -0.3381    0.2812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0706    0.9376    0.1436 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5860    2.0619   -0.0043 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4871    0.9095    0.1820 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2808   -1.8404    1.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2292   -2.0328   -0.5339 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1009   -2.5374    0.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5472    1.6381   -0.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9917    2.3065   -0.6483 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6740   -0.7241    1.3251 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8402   -1.1010   -0.4264 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0488    0.9611   -0.6385 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
 10 18  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f92397d98a8>

3-Methylglutaconic acid.mol
  Mrv1652302121822452D          

 10  9  0  0  0  0            999 V2000
    1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  3 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000522

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O4/c1-4(2-5(7)8)3-6(9)10/h2H,3H2,1H3,(H,7,8)(H,9,10)/b4-2+

> <INCHI_KEY>
WKRBKYFIJPGYQC-DUXPYHPUSA-N

> <FORMULA>
C6H8O4

> <MOLECULAR_WEIGHT>
144.1253

> <EXACT_MASS>
144.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.266891782956623

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E)-3-methylpent-2-enedioic acid

> <ALOGPS_LOGP>
0.37

> <JCHEM_LOGP>
0.287270459

> <ALOGPS_LOGS>
-1.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.659788519242309

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.854151000940069

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
33.5133

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.69e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-methylglutaconic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f92397d98a8>

HMDB0000522
     RDKit          3D
3-Methylglutaconic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -0.7065   -1.7463    0.3997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0652   -0.3827    0.2504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9037    0.6154    0.1088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3418    0.4232    0.0966 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9349   -0.6731    0.2149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2046    1.5225   -0.0578 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3977   -0.3381    0.2812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0706    0.9376    0.1436 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5860    2.0619   -0.0043 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4871    0.9095    0.1820 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2808   -1.8404    1.3186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2292   -2.0328   -0.5339 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1009   -2.5374    0.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5472    1.6381   -0.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9917    2.3065   -0.6483 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6740   -0.7241    1.3251 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8402   -1.1010   -0.4264 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0488    0.9611   -0.6385 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
 10 18  1  0
M  END
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PDB for #<Metabolite:0x00007f92397d98a8>

HEADER    PROTEIN                                 12-FEB-18   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Methylglutaconic acid.mol                       
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-FEB-18         0                                  
HETATM    1  C   UNK     0       2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -1.155   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -1.155   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667   1.155   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.001  -1.155   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.667   1.155   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -4.001  -1.155   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.000   1.155   0.000  0.00  0.00           C+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    8    9                                                  
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
CONECT   10    3                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00007f92397d98a8>

COMPND    HMDB0000522
HETATM    1  C1  UNL     1      -0.707  -1.746   0.400  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.065  -0.383   0.250  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.904   0.615   0.109  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.342   0.423   0.097  1.00  0.00           C  
HETATM    5  O1  UNL     1      -2.935  -0.673   0.215  1.00  0.00           O  
HETATM    6  O2  UNL     1      -3.205   1.522  -0.058  1.00  0.00           O  
HETATM    7  C5  UNL     1       1.398  -0.338   0.281  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.071   0.938   0.144  1.00  0.00           C  
HETATM    9  O3  UNL     1       1.586   2.062  -0.004  1.00  0.00           O  
HETATM   10  O4  UNL     1       3.487   0.910   0.182  1.00  0.00           O  
HETATM   11  H1  UNL     1      -1.281  -1.840   1.319  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.229  -2.033  -0.534  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.101  -2.537   0.490  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.547   1.638  -0.006  1.00  0.00           H  
HETATM   15  H5  UNL     1      -2.992   2.306  -0.648  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.674  -0.724   1.325  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.840  -1.101  -0.426  1.00  0.00           H  
HETATM   18  H8  UNL     1       4.049   0.961  -0.639  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    3    7
CONECT    3    4   14
CONECT    4    5    5    6
CONECT    6   15
CONECT    7    8   16   17
CONECT    8    9    9   10
CONECT   10   18
END
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SMILES for #<Metabolite:0x00007f92397d98a8>

C\C(CC(O)=O)=C/C(O)=O
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INCHI for #<Metabolite:0x00007f92397d98a8>

InChI=1S/C6H8O4/c1-4(2-5(7)8)3-6(9)10/h2H,3H2,1H3,(H,7,8)(H,9,10)/b4-2+
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Synonyms
ValueSource
3-MethylglutaconateGenerator
b-MethylglutaconateHMDB
b-Methylglutaconic acidHMDB
beta-MethylglutaconateHMDB
beta-Methylglutaconic acidHMDB
Β-methylglutaconic acidHMDB
3-Methyl-2-pentenedioic acidHMDB
3E-MethylglutaconateHMDB
3-Methylglutaconic acidHMDB, MeSH
Molecular FormulaC6H8O4
Average Mass144.1253
Monoisotopic Mass144.042258744
IUPAC Name(2E)-3-methylpent-2-enedioic acid
Traditional Nameβ-methylglutaconic acid
CAS Registry NumberNot Available
SMILES
C\C(CC(O)=O)=C/C(O)=O
InChI Identifier
InChI=1S/C6H8O4/c1-4(2-5(7)8)3-6(9)10/h2H,3H2,1H3,(H,7,8)(H,9,10)/b4-2+
InChI KeyWKRBKYFIJPGYQC-DUXPYHPUSA-N