Showing metabocard for Methylsuccinic acid (MMDBc0000392)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:36:45 UTC
Update Date2024-04-30 19:32:06 UTC
Metabolite IDMMDBc0000392
Metabolite Identification
Common NameMethylsuccinic acid
DescriptionMethylsuccinic acid (CAS: 498-21-5) is a normal metabolite found in human fluids. Increased urinary levels of methylsuccinic acid (together with ethylmalonic acid) are the main biochemical measurable features in ethylmalonic encephalopathy (OMIM: 602473 ), a rare metabolic disorder with an autosomal recessive mode of inheritance that is clinically characterized by neuromotor delay, hyperlactic acidemia, recurrent petechiae, orthostatic acrocyanosis, and chronic diarrhea (PMID:12382164 ). The underlying biochemical defect involves isoleucine catabolism (PMID:9667231 ). Methylsuccinic acid levels were found to have decreased in the urine of animals under D-serine-induced nephrotoxicity (D-serine causes selective necrosis of the proximal straight tubules in the rat kidney) (PMID:15596249 ). Moreover, methylsuccinic acid is found to be associated with ethylmalonic encephalopathy, isovaleric acidemia, and medium-chain acyl-CoA dehydrogenase deficiency, which are also inborn errors of metabolism.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92010a1640>


  Mrv1652303172016322D          

  9  8  0  0  1  0            999 V2000
    1.7069   -0.0228    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8656   -0.4353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924   -1.2604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511    0.8022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778   -0.0228    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4366   -0.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778    0.8022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924   -0.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511   -0.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  9  1  0  0  0  0
  3  8  2  0  0  0  0
  4  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  6  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f92010a1640>

HMDB0001844
     RDKit          3D
Methylsuccinic acid
 17 16  0  0  0  0  0  0  0  0999 V2000
    0.9049   -0.8327   -0.6174 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4240    0.4564    0.0334 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9668    0.2498    0.6040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9147   -0.1302   -0.4693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3657    0.7916   -1.2296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3229   -1.4387   -0.6728 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3818    0.7655    1.1286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9654    0.8438    2.2975 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7169    0.9564    0.7999 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4727   -1.7283   -0.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0112   -0.9222   -0.5420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6606   -0.8798   -1.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4274    1.2222   -0.7638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3145    1.2152    1.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9665   -0.5182    1.3983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1390   -1.6380   -1.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0253    1.5873    0.0660 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  6
  3 14  1  0
  3 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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3D SDF for #<Metabolite:0x00007f92010a1640>


  Mrv1652303172016322D          

  9  8  0  0  1  0            999 V2000
    1.7069   -0.0228    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8656   -0.4353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924   -1.2604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511    0.8022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778   -0.0228    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4366   -0.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778    0.8022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9924   -0.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511   -0.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  9  1  0  0  0  0
  3  8  2  0  0  0  0
  4  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  6  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000392

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@@H](CC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O4/c1-3(5(8)9)2-4(6)7/h3H,2H2,1H3,(H,6,7)(H,8,9)/t3-/m0/s1

> <INCHI_KEY>
WXUAQHNMJWJLTG-VKHMYHEASA-N

> <FORMULA>
C5H8O4

> <MOLECULAR_WEIGHT>
132.115

> <EXACT_MASS>
132.042258738

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.866190114358801

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-methylbutanedioic acid

> <ALOGPS_LOGP>
0.13

> <JCHEM_LOGP>
0.14450331100000002

> <ALOGPS_LOGS>
-0.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.578119667709393

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9897992068502925

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
28.1115

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-methylbutanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f92010a1640>

HMDB0001844
     RDKit          3D
Methylsuccinic acid
 17 16  0  0  0  0  0  0  0  0999 V2000
    0.9049   -0.8327   -0.6174 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4240    0.4564    0.0334 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9668    0.2498    0.6040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9147   -0.1302   -0.4693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3657    0.7916   -1.2296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3229   -1.4387   -0.6728 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3818    0.7655    1.1286 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9654    0.8438    2.2975 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7169    0.9564    0.7999 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4727   -1.7283   -0.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0112   -0.9222   -0.5420 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6606   -0.8798   -1.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4274    1.2222   -0.7638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3145    1.2152    1.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9665   -0.5182    1.3983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1390   -1.6380   -1.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0253    1.5873    0.0660 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  6
  3 14  1  0
  3 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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PDB for #<Metabolite:0x00007f92010a1640>

HEADER    PROTEIN                                 17-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAR-20         0                                  
HETATM    1  O   UNK     0       3.186  -0.043   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      -3.483  -0.813   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       1.852  -2.353   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -2.149   1.497   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.519  -0.043   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.815  -0.813   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.519   1.497   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.852  -0.813   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.149  -0.043   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3    8                                                            
CONECT    4    9                                                            
CONECT    5    6    7    8                                                  
CONECT    6    5    9                                                       
CONECT    7    5                                                            
CONECT    8    1    3    5                                                  
CONECT    9    2    4    6                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x00007f92010a1640>

COMPND    HMDB0001844
HETATM    1  C1  UNL     1       0.905  -0.833  -0.617  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.424   0.456   0.033  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.967   0.250   0.604  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.915  -0.130  -0.469  1.00  0.00           C  
HETATM    5  O1  UNL     1      -2.366   0.792  -1.230  1.00  0.00           O  
HETATM    6  O2  UNL     1      -2.323  -1.439  -0.673  1.00  0.00           O  
HETATM    7  C5  UNL     1       1.382   0.765   1.129  1.00  0.00           C  
HETATM    8  O3  UNL     1       0.965   0.844   2.297  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.717   0.956   0.800  1.00  0.00           O  
HETATM   10  H1  UNL     1       0.473  -1.728  -0.111  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.011  -0.922  -0.542  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.661  -0.880  -1.700  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.427   1.222  -0.764  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.314   1.215   1.007  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.967  -0.518   1.398  1.00  0.00           H  
HETATM   16  H7  UNL     1      -3.139  -1.638  -1.229  1.00  0.00           H  
HETATM   17  H8  UNL     1       3.025   1.587   0.066  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    7   13
CONECT    3    4   14   15
CONECT    4    5    5    6
CONECT    6   16
CONECT    7    8    8    9
CONECT    9   17
END
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SMILES for #<Metabolite:0x00007f92010a1640>

C[C@@H](CC(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f92010a1640>

InChI=1S/C5H8O4/c1-3(5(8)9)2-4(6)7/h3H,2H2,1H3,(H,6,7)(H,8,9)/t3-/m0/s1
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Synonyms
ValueSource
(S)-2-Methylbutanedioic acidChEBI
(S)-2-MethylbutanedioateGenerator
MethylsuccinateGenerator
(S)-MethylsuccinateHMDB
(-)-(2S)-Methylbutanedioic acidHMDB
(-)-(S)-alpha-Methylsuccinic acidHMDB
(-)-(S)-Α-methylsuccinic acidHMDB
(-)-2-Methylsuccinic acidHMDB
(-)-Methylsuccinic acidHMDB
(-)-alpha-Methylsuccinic acidHMDB
(-)-Α-methylsuccinic acidHMDB
(2S)-2-Methylbutanedioic acidHMDB
(2S)-Methylbutanedioic acidHMDB
(S)-(-)-2-Methylsuccinic acidHMDB
(S)-(-)-Methylsuccinic acidHMDB
(S)-2-Methylsuccinic acidHMDB
(S)-Methylsuccinic acidHMDB
(S)-alpha-Methylsuccinic acidHMDB
(S)-Α-methylsuccinic acidHMDB
1,2-Propanedicarboxylic acidHMDB
2-Methylbutane-1,4-dioic acidHMDB
2-Methylbutanedioic acidHMDB
2-Methylsuccinic acidHMDB
Methylbutanedioic acidHMDB
Pyrotartaric acidHMDB
alpha-Methylsuccinic acidHMDB
Α-methylsuccinic acidHMDB
Methylsuccinic acidHMDB
Molecular FormulaC5H8O4
Average Mass132.115
Monoisotopic Mass132.042258738
IUPAC Name(2S)-2-methylbutanedioic acid
Traditional Name(2S)-2-methylbutanedioic acid
CAS Registry NumberNot Available
SMILES
C[C@@H](CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O4/c1-3(5(8)9)2-4(6)7/h3H,2H2,1H3,(H,6,7)(H,8,9)/t3-/m0/s1
InChI KeyWXUAQHNMJWJLTG-VKHMYHEASA-N