Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-02-26 19:00:44 UTC

Update Date

2022-03-07 03:17:35 UTC

HMDB ID

HMDB0059729

Secondary Accession Numbers

HMDB59729

Metabolite Identification

Common Name

3,4-Methylenesebacic acid

Description

3,4-Methylenesebacic acid belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. 3,4-Methylenesebacic acid is a weakly acidic compound (based on its pKa).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0059729
     RDKit          3D
3,4-Methylenesebacic acid
 34 33  0  0  0  0  0  0  0  0999 V2000
    1.0922    1.6349   -0.8838 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1203    0.3405   -0.7525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0617   -0.4502   -1.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8509   -1.0152    0.0197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4527    0.0121    0.9537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4107    0.9432    0.2810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5761    0.2241   -0.3262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4099   -0.5364    0.6031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2791   -0.6265    1.8437 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4783   -1.2473    0.0483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3656   -0.3080   -0.2497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3592   -1.6134   -0.1711 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4698    0.5843    0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7125    0.0509    0.5541 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0083   -1.1334    0.6963 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7337    0.9786    0.8813 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9466    2.2223   -0.6286 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2220    2.1300   -1.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7492    0.1714   -1.7355 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2026   -1.3245   -1.7690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3213   -1.7410    0.6539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7305   -1.5447   -0.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6635    0.5536    1.5265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0010   -0.5685    1.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7753    1.7264    1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9353    1.5163   -0.5540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2236   -0.4455   -1.1432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2470    0.9545   -0.8824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6838   -1.2967   -0.9246 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2085   -2.1546    0.1816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5121   -2.2218   -0.4842 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6894    1.2051   -0.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0677    1.3969    0.8133 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1393    1.5827    0.1881 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  2 11  1  0
 11 12  2  3
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
 10 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 13 33  1  0
 16 34  1  0
M  END


  Mrv0541 02261312002D          

 16 15  0  0  0  0            999 V2000
    3.5211    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    4.0954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6645    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3789    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0934    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8079    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5224    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5224    4.0954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2368    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2368    2.0329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9513    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3802    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.0329    0.0000 O   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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059729

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H18O4/c1-9(10(2)8-12(15)16)6-4-3-5-7-11(13)14/h1-8H2,(H,13,14)(H,15,16)

> <INCHI_KEY>
YVOCTABTPCVYNG-UHFFFAOYSA-N

> <FORMULA>
C12H18O4

> <MOLECULAR_WEIGHT>
226.2689

> <EXACT_MASS>
226.120509064

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
24.362427658591564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,4-dimethylidenedecanedioic acid

> <ALOGPS_LOGP>
2.08

> <JCHEM_LOGP>
2.147675593333333

> <ALOGPS_LOGS>
-2.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.2615983807684765

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.656979125707469

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
59.795199999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.61e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dimethylidenedecanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0059729
     RDKit          3D
3,4-Methylenesebacic acid
 34 33  0  0  0  0  0  0  0  0999 V2000
    1.0922    1.6349   -0.8838 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1203    0.3405   -0.7525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0617   -0.4502   -1.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8509   -1.0152    0.0197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4527    0.0121    0.9537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4107    0.9432    0.2810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5761    0.2241   -0.3262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4099   -0.5364    0.6031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2791   -0.6265    1.8437 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4783   -1.2473    0.0483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3656   -0.3080   -0.2497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3592   -1.6134   -0.1711 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4698    0.5843    0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7125    0.0509    0.5541 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0083   -1.1334    0.6963 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7337    0.9786    0.8813 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9466    2.2223   -0.6286 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2220    2.1300   -1.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7492    0.1714   -1.7355 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2026   -1.3245   -1.7690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3213   -1.7410    0.6539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7305   -1.5447   -0.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6635    0.5536    1.5265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0010   -0.5685    1.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7753    1.7264    1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9353    1.5163   -0.5540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2236   -0.4455   -1.1432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2470    0.9545   -0.8824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6838   -1.2967   -0.9246 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2085   -2.1546    0.1816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5121   -2.2218   -0.4842 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6894    1.2051   -0.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0677    1.3969    0.8133 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1393    1.5827    0.1881 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  2 11  1  0
 11 12  2  3
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
 10 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 13 33  1  0
 16 34  1  0
M  END

HEADER    PROTEIN                                 26-FEB-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-FEB-13         0                                  
HETATM    1  O   UNK     0       6.573   5.335   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.906   6.105   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       7.906   7.645   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       9.240   5.335   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.574   6.105   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.907   5.335   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.241   6.105   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.575   5.335   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.908   6.105   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      15.908   7.645   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.242   5.335   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      17.242   3.795   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      18.576   6.105   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      19.909   5.335   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      21.243   6.105   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      19.909   3.795   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

COMPND    HMDB0059729
HETATM    1  C1  UNL     1       1.092   1.635  -0.884  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.120   0.341  -0.753  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.062  -0.450  -1.107  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.851  -1.015   0.020  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.453   0.012   0.954  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.411   0.943   0.281  1.00  0.00           C  
HETATM    7  C7  UNL     1      -3.576   0.224  -0.326  1.00  0.00           C  
HETATM    8  C8  UNL     1      -4.410  -0.536   0.603  1.00  0.00           C  
HETATM    9  O1  UNL     1      -4.279  -0.627   1.844  1.00  0.00           O  
HETATM   10  O2  UNL     1      -5.478  -1.247   0.048  1.00  0.00           O  
HETATM   11  C9  UNL     1       2.366  -0.308  -0.250  1.00  0.00           C  
HETATM   12  C10 UNL     1       2.359  -1.613  -0.171  1.00  0.00           C  
HETATM   13  C11 UNL     1       3.470   0.584   0.102  1.00  0.00           C  
HETATM   14  C12 UNL     1       4.713   0.051   0.554  1.00  0.00           C  
HETATM   15  O3  UNL     1       5.008  -1.133   0.696  1.00  0.00           O  
HETATM   16  O4  UNL     1       5.734   0.979   0.881  1.00  0.00           O  
HETATM   17  H1  UNL     1       1.947   2.222  -0.629  1.00  0.00           H  
HETATM   18  H2  UNL     1       0.222   2.130  -1.252  1.00  0.00           H  
HETATM   19  H3  UNL     1      -0.749   0.171  -1.736  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.203  -1.325  -1.769  1.00  0.00           H  
HETATM   21  H5  UNL     1      -0.321  -1.741   0.654  1.00  0.00           H  
HETATM   22  H6  UNL     1      -1.730  -1.545  -0.454  1.00  0.00           H  
HETATM   23  H7  UNL     1      -0.663   0.554   1.526  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.001  -0.568   1.720  1.00  0.00           H  
HETATM   25  H9  UNL     1      -2.775   1.726   1.005  1.00  0.00           H  
HETATM   26  H10 UNL     1      -1.935   1.516  -0.554  1.00  0.00           H  
HETATM   27  H11 UNL     1      -3.224  -0.445  -1.143  1.00  0.00           H  
HETATM   28  H12 UNL     1      -4.247   0.955  -0.882  1.00  0.00           H  
HETATM   29  H13 UNL     1      -5.684  -1.297  -0.925  1.00  0.00           H  
HETATM   30  H14 UNL     1       3.208  -2.155   0.182  1.00  0.00           H  
HETATM   31  H15 UNL     1       1.512  -2.222  -0.484  1.00  0.00           H  
HETATM   32  H16 UNL     1       3.689   1.205  -0.835  1.00  0.00           H  
HETATM   33  H17 UNL     1       3.068   1.397   0.813  1.00  0.00           H  
HETATM   34  H18 UNL     1       6.139   1.583   0.188  1.00  0.00           H  
CONECT    1    2    2   17   18
CONECT    2    3   11
CONECT    3    4   19   20
CONECT    4    5   21   22
CONECT    5    6   23   24
CONECT    6    7   25   26
CONECT    7    8   27   28
CONECT    8    9    9   10
CONECT   10   29
CONECT   11   12   12   13
CONECT   12   30   31
CONECT   13   14   32   33
CONECT   14   15   15   16
CONECT   16   34
END

HMDB0059729
     RDKit          3D
3,4-Methylenesebacic acid
 34 33  0  0  0  0  0  0  0  0999 V2000
    1.0922    1.6349   -0.8838 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1203    0.3405   -0.7525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0617   -0.4502   -1.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8509   -1.0152    0.0197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4527    0.0121    0.9537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4107    0.9432    0.2810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5761    0.2241   -0.3262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4099   -0.5364    0.6031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2791   -0.6265    1.8437 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4783   -1.2473    0.0483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3656   -0.3080   -0.2497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3592   -1.6134   -0.1711 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4698    0.5843    0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7125    0.0509    0.5541 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0083   -1.1334    0.6963 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7337    0.9786    0.8813 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9466    2.2223   -0.6286 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2220    2.1300   -1.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7492    0.1714   -1.7355 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2026   -1.3245   -1.7690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3213   -1.7410    0.6539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7305   -1.5447   -0.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6635    0.5536    1.5265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0010   -0.5685    1.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7753    1.7264    1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9353    1.5163   -0.5540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2236   -0.4455   -1.1432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2470    0.9545   -0.8824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6838   -1.2967   -0.9246 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2085   -2.1546    0.1816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5121   -2.2218   -0.4842 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6894    1.2051   -0.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0677    1.3969    0.8133 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1393    1.5827    0.1881 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  2 11  1  0
 11 12  2  3
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
 10 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 13 33  1  0
 16 34  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3,4-Methylenesebacate	Generator
3,4-Dimethylidenedecanedioate	Generator

Chemical Formula

C₁₂H₁₈O₄

Average Molecular Weight

226.2689

Monoisotopic Molecular Weight

226.120509064

IUPAC Name

3,4-dimethylidenedecanedioic acid

Traditional Name

3,4-dimethylidenedecanedioic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CCCCCC(=C)C(=C)CC(O)=O

InChI Identifier

InChI=1S/C12H18O4/c1-9(10(2)8-12(15)16)6-4-3-5-7-11(13)14/h1-8H2,(H,13,14)(H,15,16)

InChI Key

YVOCTABTPCVYNG-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Branched fatty acid
Unsaturated fatty acid
Dicarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Urine (PMID: 2338430)

Cellular substructure

Membrane (HMDB: HMDB0059729)

Source

Exogenous

Exogenous (HMDB: HMDB0059729)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.66 g/L	ALOGPS
logP	2.08	ALOGPS
logP	2.15	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	4.66	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	59.8 m³·mol⁻¹	ChemAxon
Polarizability	24.36 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	156.176	31661259
DarkChem	[M-H]-	150.099	31661259
DeepCCS	[M+H]+	149.86	30932474
DeepCCS	[M-H]-	146.739	30932474
DeepCCS	[M-2H]-	183.737	30932474
DeepCCS	[M+Na]+	159.277	30932474
AllCCS	[M+H]+	156.5	32859911
AllCCS	[M+H-H2O]+	153.0	32859911
AllCCS	[M+NH4]+	159.8	32859911
AllCCS	[M+Na]+	160.7	32859911
AllCCS	[M-H]-	154.1	32859911
AllCCS	[M+Na-2H]-	155.0	32859911
AllCCS	[M+HCOO]-	156.1	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm √ó 2.1 mm; 1.7 Œºmparticle diameter). Predicted by Afia on May 17, 2022.	6.01 minutes	32390414
Predicted by Siyang on May 30, 2022	12.4408 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.46 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1929.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	324.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	144.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	189.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	215.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	419.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	524.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	100.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1073.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	409.1 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1323.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	349.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	346.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	403.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	248.0 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	84.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3,4-Methylenesebacic acid	OC(=O)CCCCCC(=C)C(=C)CC(O)=O	2885.1	Standard polar	33892256
3,4-Methylenesebacic acid	OC(=O)CCCCCC(=C)C(=C)CC(O)=O	1596.2	Standard non polar	33892256
3,4-Methylenesebacic acid	OC(=O)CCCCCC(=C)C(=C)CC(O)=O	1917.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3,4-Methylenesebacic acid,1TMS,isomer #1	C=C(CCCCCC(=O)O[Si](C)(C)C)C(=C)CC(=O)O	1846.0	Semi standard non polar	33892256
3,4-Methylenesebacic acid,1TMS,isomer #2	C=C(CCCCCC(=O)O)C(=C)CC(=O)O[Si](C)(C)C	1855.7	Semi standard non polar	33892256
3,4-Methylenesebacic acid,2TMS,isomer #1	C=C(CCCCCC(=O)O[Si](C)(C)C)C(=C)CC(=O)O[Si](C)(C)C	1944.6	Semi standard non polar	33892256
3,4-Methylenesebacic acid,1TBDMS,isomer #1	C=C(CCCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=C)CC(=O)O	2070.8	Semi standard non polar	33892256
3,4-Methylenesebacic acid,1TBDMS,isomer #2	C=C(CCCCCC(=O)O)C(=C)CC(=O)O[Si](C)(C)C(C)(C)C	2085.8	Semi standard non polar	33892256
3,4-Methylenesebacic acid,2TBDMS,isomer #1	C=C(CCCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=C)CC(=O)O[Si](C)(C)C(C)(C)C	2405.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Methylenesebacic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-00l6-4910000000-d61706721baa16cd2056	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Methylenesebacic acid GC-MS (2 TMS) - 70eV, Positive	splash10-0079-9271000000-e892d7d779d7ebc64727	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Methylenesebacic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Methylenesebacic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 10V, Positive-QTOF	splash10-0a4i-0690000000-e980bab2f044d1d279cf	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 20V, Positive-QTOF	splash10-07d0-0910000000-3b4e1f9b8d1bbd58977d	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 40V, Positive-QTOF	splash10-0avu-9700000000-ddacb31c81dec0055dd3	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 10V, Negative-QTOF	splash10-057i-0590000000-90db2fa92f03b6d4556b	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 20V, Negative-QTOF	splash10-0a7i-1790000000-20491865363810446d45	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 40V, Negative-QTOF	splash10-0a4i-9610000000-8dd67c9e1bef4700ab85	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 10V, Negative-QTOF	splash10-0a6r-0090000000-84b70b86250d7cafb8a3	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 20V, Negative-QTOF	splash10-0a70-2970000000-531ca87dbd25312f5e3d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 40V, Negative-QTOF	splash10-0aor-9500000000-d3beb140191756ff47f4	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 10V, Positive-QTOF	splash10-056r-1950000000-3cd6153e5f6ecd680f97	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 20V, Positive-QTOF	splash10-05oy-8900000000-53be8864242b4d71831c	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenesebacic acid 40V, Positive-QTOF	splash10-0693-9100000000-161267a8fabcf071b7d3	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	2338430	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

124202122

PDB ID

Not Available

ChEBI ID

89935

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for 3,4-Methylenesebacic acid (HMDB0059729)

MOL for HMDB0059729 (3,4-Methylenesebacic acid)

3D MOL for HMDB0059729 (3,4-Methylenesebacic acid)

3D SDF for HMDB0059729 (3,4-Methylenesebacic acid)

3D-SDF for HMDB0059729 (3,4-Methylenesebacic acid)

PDB for HMDB0059729 (3,4-Methylenesebacic acid)

3D PDB for HMDB0059729 (3,4-Methylenesebacic acid)

SMILES for HMDB0059729 (3,4-Methylenesebacic acid)

INCHI for HMDB0059729 (3,4-Methylenesebacic acid)

Structure for HMDB0059729 (3,4-Methylenesebacic acid)

3D Structure for HMDB0059729 (3,4-Methylenesebacic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra