Showing metabocard for Methyl succinate (MMDBc0033682)

Xenobiotic
Record Information
Version2.0
StatusDetected and Quantified
Creation Date2021-11-19 04:58:48 UTC
Update Date2025-10-07 16:08:02 UTC
Metabolite IDMMDBc0033682
Metabolite Identification
Common NameMethyl succinate
DescriptionMethyl succinate is a dicarboxylic acid ester belonging to the class of organic compounds known as succinates. Its chemical structure consists of a succinate backbone with a methyl group esterified at one of the carboxylic acid functional groups, resulting in the formula C5H8O4. Methyl succinate plays a role in various metabolic pathways, including those related to energy production and amino acid metabolism. For instance, it has been identified as a significant metabolite in studies examining metabolic differences among subjects (PMID:40863139 ) and is associated with increased levels of other metabolites in response to dietary factors (PMID:39637305 ). Additionally, methyl succinate is involved in the synthesis of biodegradable polymers, such as poly(butylene succinate-co-2-methyl succinate), which have applications in materials science (PMID:38932085 ). It also appears in metabolic analyses highlighting its potential link to inflammatory activities and antioxidant properties (PMID:38392978 ). Furthermore, its derivatives, such as monomethyl succinate, are noted as major urinary metabolites in pharmacokinetic studies (PMID:37216617 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9ab117ef28>


  Mrv0541 02241223242D          

  9  8  0  0  0  0            999 V2000
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f9ab117ef28>

HMDB0253609
     RDKit          3D
Isobutyl acrylate
 21 20  0  0  0  0  0  0  0  0999 V2000
    4.1533   -0.6061   -0.1954 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8894   -0.7520   -0.5555 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8434   -0.0073    0.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1724    0.7535    1.1090 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5086   -0.0983   -0.1413 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4402    0.6462    0.5933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8478    0.4269    0.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0562    0.8100   -1.3130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3318   -0.9722    0.4330 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4438    0.0530    0.6234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9480   -1.1295   -0.6927 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6609   -1.4139   -1.3684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1995    1.7250    0.5144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4188    0.3857    1.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4932    1.1097    0.7342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7761    0.0317   -2.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1287    1.1236   -1.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4457    1.7325   -1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4474   -0.9614    0.2778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2077   -1.1035    1.5397 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8269   -1.7535   -0.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
  8 18  1  0
  9 19  1  0
  9 20  1  0
  9 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f9ab117ef28>


  Mrv0541 02241223242D          

  9  8  0  0  0  0            999 V2000
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033682

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O2/c1-4-7(8)9-5-6(2)3/h4,6H,1,5H2,2-3H3

> <INCHI_KEY>
CFVWNXQPGQOHRJ-UHFFFAOYSA-N

> <FORMULA>
C7H12O2

> <MOLECULAR_WEIGHT>
128.169

> <EXACT_MASS>
128.083729628

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
14.227572109265818

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylpropyl prop-2-enoate

> <ALOGPS_LOGP>
2.14

> <JCHEM_LOGP>
2.1564778579999997

> <ALOGPS_LOGS>
-1.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.7807671484732905

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
35.8047

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.15e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isobutyl acrylate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for #<Metabolite:0x00007f9ab117ef28>

HMDB0253609
     RDKit          3D
Isobutyl acrylate
 21 20  0  0  0  0  0  0  0  0999 V2000
    4.1533   -0.6061   -0.1954 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8894   -0.7520   -0.5555 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8434   -0.0073    0.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1724    0.7535    1.1090 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5086   -0.0983   -0.1413 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4402    0.6462    0.5933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8478    0.4269    0.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0562    0.8100   -1.3130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3318   -0.9722    0.4330 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4438    0.0530    0.6234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9480   -1.1295   -0.6927 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6609   -1.4139   -1.3684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1995    1.7250    0.5144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4188    0.3857    1.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4932    1.1097    0.7342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7761    0.0317   -2.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1287    1.1236   -1.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4457    1.7325   -1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4474   -0.9614    0.2778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2077   -1.1035    1.5397 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8269   -1.7535   -0.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
  8 18  1  0
  9 19  1  0
  9 20  1  0
  9 21  1  0
M  END
Download

PDB for #<Metabolite:0x00007f9ab117ef28>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       7.287   2.667   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.620   1.127   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    2    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
Download

3D PDB for #<Metabolite:0x00007f9ab117ef28>

COMPND    HMDB0253609
HETATM    1  C1  UNL     1       4.153  -0.606  -0.195  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.889  -0.752  -0.556  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.843  -0.007   0.165  1.00  0.00           C  
HETATM    4  O1  UNL     1       2.172   0.753   1.109  1.00  0.00           O  
HETATM    5  O2  UNL     1       0.509  -0.098  -0.141  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.440   0.646   0.593  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.848   0.427   0.125  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.056   0.810  -1.313  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.332  -0.972   0.433  1.00  0.00           C  
HETATM   10  H1  UNL     1       4.444   0.053   0.623  1.00  0.00           H  
HETATM   11  H2  UNL     1       4.948  -1.130  -0.693  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.661  -1.414  -1.368  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.199   1.725   0.514  1.00  0.00           H  
HETATM   14  H5  UNL     1      -0.419   0.386   1.683  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.493   1.110   0.734  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.776   0.032  -2.029  1.00  0.00           H  
HETATM   17  H8  UNL     1      -3.129   1.124  -1.430  1.00  0.00           H  
HETATM   18  H9  UNL     1      -1.446   1.732  -1.492  1.00  0.00           H  
HETATM   19  H10 UNL     1      -3.447  -0.961   0.278  1.00  0.00           H  
HETATM   20  H11 UNL     1      -2.208  -1.103   1.540  1.00  0.00           H  
HETATM   21  H12 UNL     1      -1.827  -1.754  -0.127  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4    4    5
CONECT    5    6
CONECT    6    7   13   14
CONECT    7    8    9   15
CONECT    8   16   17   18
CONECT    9   19   20   21
END
Download

SMILES for #<Metabolite:0x00007f9ab117ef28>

CC(C)COC(=O)C=C
Download

INCHI for #<Metabolite:0x00007f9ab117ef28>

InChI=1S/C7H12O2/c1-4-7(8)9-5-6(2)3/h4,6H,1,5H2,2-3H3
Download
Synonyms
ValueSource
Methyl succinic acidGenerator
Molecular FormulaC7H12O2
Average Mass128.169
Monoisotopic Mass128.083729628
IUPAC Name2-methylpropyl prop-2-enoate
Traditional Nameisobutyl acrylate
CAS Registry Number106-65-0
SMILES
CC(C)COC(=O)C=C
InChI Identifier
InChI=1S/C7H12O2/c1-4-7(8)9-5-6(2)3/h4,6H,1,5H2,2-3H3
InChI KeyCFVWNXQPGQOHRJ-UHFFFAOYSA-N