Showing metabocard for Methylmalonic acid (MMDBc0000502)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:13 UTC
Update Date2022-08-31 06:07:42 UTC
Metabolite IDMMDBc0000502
Metabolite Identification
Common NameMethylmalonic acid
DescriptionMethylmalonic acid is a malonic acid derivative, which is a vital intermediate in the metabolism of fat and protein. In particular, the coenzyme A-linked form of methylmalonic acid, methylmalonyl-CoA, is converted into succinyl-CoA by methylmalonyl-CoA mutase in a reaction that requires vitamin B12 as a cofactor. In this way, methylmalonic acid enters the Krebs cycle and is thus part of one of the anaplerotic reactions. Abnormalities in methylmalonic acid metabolism lead to methylmalonic aciduria. This inborn error of metabolism is attributed to a block in the enzymatic conversion of methylmalonyl CoA to succinyl CoA. Methylmalonic acid is also found to be associated with other inborn errors of metabolism, including cobalamin deficiency, cobalamin malabsorption, malonyl-CoA decarboxylase deficiency, and transcobalamin II deficiency. When present in sufficiently high levels, methylmalonic 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 methylmalonic acid are associated with at least 5 inborn errors of metabolism, including Malonyl CoA decarboxylase deficiency, Malonic Aciduria, Methylmalonate Semialdehyde Dehydrogenase Deficiency, Methylmalonic Aciduria and Methylmalonic Aciduria Due to Cobalamin-Related Disorders. Methylmalonic acid is an organic acid and 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 abnormalities, kidney abnormalities, liver damage, 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:0x00007f124059ad68>


  Mrv1652305271900212D          

  8  7  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   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  2  0  0  0  0
  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f124059ad68>

HMDB0000202
     RDKit          3D
Methylmalonic acid
 14 13  0  0  0  0  0  0  0  0999 V2000
   -0.0713   -0.4912    1.2791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1048   -0.3766   -0.2320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9010    0.8030   -0.5919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3350    1.7138   -1.2495 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2207    0.9632   -0.2511 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2455   -0.3645   -0.8307 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5790   -1.2719   -1.6650 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1941    0.5808   -0.5449 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1102    0.4838    1.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9342   -1.1118    1.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8573   -1.0216    1.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6628   -1.2733   -0.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9927    0.4363   -0.6617 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4569    0.9300    0.3448 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  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
  5 13  1  0
  8 14  1  0
M  END
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3D SDF for #<Metabolite:0x00007f124059ad68>


  Mrv1652305271900212D          

  8  7  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   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  2  0  0  0  0
  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000502

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)

> <INCHI_KEY>
ZIYVHBGGAOATLY-UHFFFAOYSA-N

> <FORMULA>
C4H6O4

> <MOLECULAR_WEIGHT>
118.088

> <EXACT_MASS>
118.02660868

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.057853065917067

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylpropanedioic acid

> <ALOGPS_LOGP>
0.17

> <JCHEM_LOGP>
0.21186901000000008

> <ALOGPS_LOGS>
0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.256772105384455

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4752703991264853

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
23.5623

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylmalonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f124059ad68>

HMDB0000202
     RDKit          3D
Methylmalonic acid
 14 13  0  0  0  0  0  0  0  0999 V2000
   -0.0713   -0.4912    1.2791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1048   -0.3766   -0.2320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9010    0.8030   -0.5919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3350    1.7138   -1.2495 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2207    0.9632   -0.2511 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2455   -0.3645   -0.8307 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5790   -1.2719   -1.6650 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1941    0.5808   -0.5449 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1102    0.4838    1.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9342   -1.1118    1.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8573   -1.0216    1.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6628   -1.2733   -0.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9927    0.4363   -0.6617 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4569    0.9300    0.3448 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  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
  5 13  1  0
  8 14  1  0
M  END
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PDB for #<Metabolite:0x00007f124059ad68>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.000   2.667   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f124059ad68>

COMPND    HMDB0000202
HETATM    1  C1  UNL     1      -0.071  -0.491   1.279  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.105  -0.377  -0.232  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.901   0.803  -0.592  1.00  0.00           C  
HETATM    4  O1  UNL     1      -0.335   1.714  -1.249  1.00  0.00           O  
HETATM    5  O2  UNL     1      -2.221   0.963  -0.251  1.00  0.00           O  
HETATM    6  C4  UNL     1       1.246  -0.364  -0.831  1.00  0.00           C  
HETATM    7  O3  UNL     1       1.579  -1.272  -1.665  1.00  0.00           O  
HETATM    8  O4  UNL     1       2.194   0.581  -0.545  1.00  0.00           O  
HETATM    9  H1  UNL     1      -0.110   0.484   1.786  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.934  -1.112   1.651  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.857  -1.022   1.559  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.663  -1.273  -0.594  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.993   0.436  -0.662  1.00  0.00           H  
HETATM   14  H6  UNL     1       2.457   0.930   0.345  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    6   12
CONECT    3    4    4    5
CONECT    5   13
CONECT    6    7    7    8
CONECT    8   14
END
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SMILES for #<Metabolite:0x00007f124059ad68>

CC(C(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f124059ad68>

InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)
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Synonyms
ValueSource
1,1-Ethanedicarboxylic acidChEBI
2-Methylmalonic acidChEBI
alpha-Methylmalonic acidChEBI
Isosuccinic acidChEBI
1,1-EthanedicarboxylateGenerator
2-MethylmalonateGenerator
a-MethylmalonateGenerator
a-Methylmalonic acidGenerator
alpha-MethylmalonateGenerator
Α-methylmalonateGenerator
Α-methylmalonic acidGenerator
IsosuccinateGenerator
MethylmalonateGenerator
Methyl-malonateHMDB
Methyl-malonic acidHMDB
Methyl-propanedioateHMDB
Methyl-propanedioic acidHMDB
MethylpropanedioateHMDB
Methylpropanedioic acidHMDB
Acid, methylmalonicHMDB
Methylmalonic acidKEGG
Molecular FormulaC4H6O4
Average Mass118.088
Monoisotopic Mass118.02660868
IUPAC Name2-methylpropanedioic acid
Traditional Namemethylmalonic acid
CAS Registry NumberNot Available
SMILES
CC(C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)
InChI KeyZIYVHBGGAOATLY-UHFFFAOYSA-N