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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2025-03-14 16:33:31 UTC

HMDB ID

HMDB0000603

Secondary Accession Numbers

HMDB00603

Metabolite Identification

Common Name

cis-4-Decenedioic acid

Description

cis-4-Decenedioic acid is a member of the class of compounds known as medium-chain fatty acids. Medium-chain fatty acids are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. Thus, cis-4-decenedioic acid is considered to be a fatty acid lipid molecule. Cis-4-decenedioic acid is slightly soluble (in water) and a weakly acidic compound (based on its pKa). Cis-4-decenedioic acid can be found primarily in urine. Within the cell, cis-4-decenedioic acid is primarily located in the membrane. It can also be found in the extracellular space. Moreover, cis-4-decenedioic acid is an unsaturated dicarboxylic acid. Its level increases in patients with medium chain acyl-CoA dehydrogenase deficiency (MCADD), which is a genetic disorder of fatty acid oxidation.

Structure

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

HMDB0000603
     RDKit          3D
cis-4-Decenedioic acid
 30 29  0  0  0  0  0  0  0  0999 V2000
   -5.1880   -0.5227   -1.8080 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0746   -0.2199   -1.2404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0541   -1.1512   -1.2650 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9276    1.0909   -0.5926 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5724    1.3049    0.0159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2386    0.3200    1.0483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1884   -0.4581    0.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1649   -0.5301   -0.0639 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2282   -0.2273    0.4748 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2604   -0.3082   -0.6130 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6026    0.0008   -0.0079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6583   -0.0643   -1.0295 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3549   -0.3475   -2.2054 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0048    0.1797   -0.7410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1489   -1.9730   -0.7017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0251    1.8614   -1.4134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7522    1.2771    0.1430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8467    1.2664   -0.8085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5917    2.3300    0.4836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8915    0.2090    1.9406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0715   -1.1571    1.8449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1652   -1.5816   -0.4715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3177    0.1466   -0.9004 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2677    0.7803    0.9346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5165   -0.9553    1.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2938   -1.3275   -1.0552 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0608    0.4144   -1.4376 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8054   -0.7436    0.8101 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6216    0.9865    0.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5442   -0.6006   -0.3386 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 14 30  1  0
M  END


  Mrv1652305231918432D          

 14 13  0  0  0  0            999 V2000
   11.9693  -13.1121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5567  -13.8266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7317  -13.8264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3191  -14.5403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4941  -14.5402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0815  -15.2547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5568  -12.3976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7943  -13.1122    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2565  -15.2547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8441  -14.5402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0191  -14.5401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6066  -13.8256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7816  -13.8255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0192  -13.1112    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  2  0  0  0  0
  6  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000603

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CCCC\C=C/CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1,3H,2,4-8H2,(H,11,12)(H,13,14)/b3-1-

> <INCHI_KEY>
CXGDCGIPEJKSCK-IWQZZHSRSA-N

> <FORMULA>
C10H16O4

> <MOLECULAR_WEIGHT>
200.2316

> <EXACT_MASS>
200.104859

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
21.30100913133963

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4Z)-dec-4-enedioic acid

> <ALOGPS_LOGP>
1.83

> <JCHEM_LOGP>
1.9070073659999993

> <ALOGPS_LOGS>
-2.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.254186663752224

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.652116140475578

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
52.259600000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.31e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4Z)-dec-4-enedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000603
     RDKit          3D
cis-4-Decenedioic acid
 30 29  0  0  0  0  0  0  0  0999 V2000
   -5.1880   -0.5227   -1.8080 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0746   -0.2199   -1.2404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0541   -1.1512   -1.2650 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9276    1.0909   -0.5926 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5724    1.3049    0.0159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2386    0.3200    1.0483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1884   -0.4581    0.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1649   -0.5301   -0.0639 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2282   -0.2273    0.4748 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2604   -0.3082   -0.6130 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6026    0.0008   -0.0079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6583   -0.0643   -1.0295 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3549   -0.3475   -2.2054 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0048    0.1797   -0.7410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1489   -1.9730   -0.7017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0251    1.8614   -1.4134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7522    1.2771    0.1430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8467    1.2664   -0.8085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5917    2.3300    0.4836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8915    0.2090    1.9406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0715   -1.1571    1.8449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1652   -1.5816   -0.4715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3177    0.1466   -0.9004 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2677    0.7803    0.9346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5165   -0.9553    1.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2938   -1.3275   -1.0552 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0608    0.4144   -1.4376 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8054   -0.7436    0.8101 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6216    0.9865    0.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5442   -0.6006   -0.3386 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 14 30  1  0
M  END

HEADER    PROTEIN                                 23-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAY-19         0                                  
HETATM    1  C   UNK     0      22.343 -24.476   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.573 -25.810   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      20.033 -25.809   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      19.262 -27.142   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.722 -27.142   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.952 -28.475   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      21.573 -23.142   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      23.883 -24.476   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      15.412 -28.475   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.642 -27.142   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.102 -27.142   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.332 -25.808   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      10.792 -25.808   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      13.103 -24.474   0.000  0.00  0.00           O+0
CONECT    1    2    7    8                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    9                                                       
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    6   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

COMPND    HMDB0000603
HETATM    1  O1  UNL     1      -5.188  -0.523  -1.808  1.00  0.00           O  
HETATM    2  C1  UNL     1      -4.075  -0.220  -1.240  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.054  -1.151  -1.265  1.00  0.00           O  
HETATM    4  C2  UNL     1      -3.928   1.091  -0.593  1.00  0.00           C  
HETATM    5  C3  UNL     1      -2.572   1.305   0.016  1.00  0.00           C  
HETATM    6  C4  UNL     1      -2.239   0.320   1.048  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.188  -0.458   0.980  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.165  -0.530  -0.064  1.00  0.00           C  
HETATM    9  C7  UNL     1       1.228  -0.227   0.475  1.00  0.00           C  
HETATM   10  C8  UNL     1       2.260  -0.308  -0.613  1.00  0.00           C  
HETATM   11  C9  UNL     1       3.603   0.001  -0.008  1.00  0.00           C  
HETATM   12  C10 UNL     1       4.658  -0.064  -1.029  1.00  0.00           C  
HETATM   13  O3  UNL     1       4.355  -0.347  -2.205  1.00  0.00           O  
HETATM   14  O4  UNL     1       6.005   0.180  -0.741  1.00  0.00           O  
HETATM   15  H1  UNL     1      -3.149  -1.973  -0.702  1.00  0.00           H  
HETATM   16  H2  UNL     1      -4.025   1.861  -1.413  1.00  0.00           H  
HETATM   17  H3  UNL     1      -4.752   1.277   0.143  1.00  0.00           H  
HETATM   18  H4  UNL     1      -1.847   1.266  -0.809  1.00  0.00           H  
HETATM   19  H5  UNL     1      -2.592   2.330   0.484  1.00  0.00           H  
HETATM   20  H6  UNL     1      -2.891   0.209   1.941  1.00  0.00           H  
HETATM   21  H7  UNL     1      -1.072  -1.157   1.845  1.00  0.00           H  
HETATM   22  H8  UNL     1      -0.165  -1.582  -0.472  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.318   0.147  -0.900  1.00  0.00           H  
HETATM   24  H10 UNL     1       1.268   0.780   0.935  1.00  0.00           H  
HETATM   25  H11 UNL     1       1.516  -0.955   1.264  1.00  0.00           H  
HETATM   26  H12 UNL     1       2.294  -1.328  -1.055  1.00  0.00           H  
HETATM   27  H13 UNL     1       2.061   0.414  -1.438  1.00  0.00           H  
HETATM   28  H14 UNL     1       3.805  -0.744   0.810  1.00  0.00           H  
HETATM   29  H15 UNL     1       3.622   0.987   0.470  1.00  0.00           H  
HETATM   30  H16 UNL     1       6.544  -0.601  -0.339  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7    7   20
CONECT    7    8   21
CONECT    8    9   22   23
CONECT    9   10   24   25
CONECT   10   11   26   27
CONECT   11   12   28   29
CONECT   12   13   13   14
CONECT   14   30
END

HMDB0000603
     RDKit          3D
cis-4-Decenedioic acid
 30 29  0  0  0  0  0  0  0  0999 V2000
   -5.1880   -0.5227   -1.8080 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0746   -0.2199   -1.2404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0541   -1.1512   -1.2650 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9276    1.0909   -0.5926 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5724    1.3049    0.0159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2386    0.3200    1.0483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1884   -0.4581    0.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1649   -0.5301   -0.0639 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2282   -0.2273    0.4748 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2604   -0.3082   -0.6130 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6026    0.0008   -0.0079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6583   -0.0643   -1.0295 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3549   -0.3475   -2.2054 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0048    0.1797   -0.7410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1489   -1.9730   -0.7017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0251    1.8614   -1.4134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7522    1.2771    0.1430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8467    1.2664   -0.8085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5917    2.3300    0.4836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8915    0.2090    1.9406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0715   -1.1571    1.8449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1652   -1.5816   -0.4715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3177    0.1466   -0.9004 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2677    0.7803    0.9346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5165   -0.9553    1.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2938   -1.3275   -1.0552 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0608    0.4144   -1.4376 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8054   -0.7436    0.8101 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6216    0.9865    0.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5442   -0.6006   -0.3386 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 11 29  1  0
 14 30  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
cis-4-Decenedioate	Generator
Decenedioate	HMDB
Decenedioic acid	HMDB
4Z-Decenedioate	HMDB

Chemical Formula

C₁₀H₁₆O₄

Average Molecular Weight

200.2316

Monoisotopic Molecular Weight

200.104859

IUPAC Name

(4Z)-dec-4-enedioic acid

Traditional Name

(4Z)-dec-4-enedioic acid

CAS Registry Number

41221-65-2

SMILES

OC(=O)CCCC\C=C/CCC(O)=O

InChI Identifier

InChI=1S/C10H16O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1,3H,2,4-8H2,(H,11,12)(H,13,14)/b3-1-

InChI Key

CXGDCGIPEJKSCK-IWQZZHSRSA-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
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

Dicarboxylic acids (LMFA01170045 )

Ontology

Not Available

Urine (PMID: 2380628)

Cellular substructure

Extracellular (HMDB: HMDB0000603)
Membrane (HMDB: HMDB0000603)

Source

Exogenous

Exogenous (HMDB: HMDB0000603)

Endogenous

Endogenous (HMDB: HMDB0000603)

Process

Not Available

Role

Industrial application

Pharmaceutical industry

Biomarker

Medium Chain Acyl Co A Dehydrogenase Deficiency (MarkerDB: MDB00000197)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	133 - 137 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	2219 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1.31 g/L	ALOGPS
logP	1.83	ALOGPS
logP	1.91	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	4.65	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	8	ChemAxon
Refractivity	52.26 m³·mol⁻¹	ChemAxon
Polarizability	21.3 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]+	148.108	31661259
DarkChem	[M-H]-	145.197	31661259
AllCCS	[M+H]+	145.932	32859911
AllCCS	[M-H]-	147.754	32859911
DeepCCS	[M+H]+	143.849	30932474
DeepCCS	[M-H]-	140.022	30932474
DeepCCS	[M-2H]-	177.365	30932474
DeepCCS	[M+Na]+	152.968	30932474
AllCCS	[M+H]+	145.9	32859911
AllCCS	[M+H-H2O]+	142.3	32859911
AllCCS	[M+NH4]+	149.3	32859911
AllCCS	[M+Na]+	150.3	32859911
AllCCS	[M-H]-	147.8	32859911
AllCCS	[M+Na-2H]-	148.9	32859911
AllCCS	[M+HCOO]-	150.3	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 × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	5.3 minutes	32390414
Predicted by Siyang on May 30, 2022	11.0139 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.07 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	57.9 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1780.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	281.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	128.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	193.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	220.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	392.0 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	381.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	123.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	934.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	376.0 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	1043.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	299.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	305.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	481.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	223.0 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	124.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
cis-4-Decenedioic acid	OC(=O)CCCC\C=C/CCC(O)=O	2800.0	Standard polar	33892256
cis-4-Decenedioic acid	OC(=O)CCCC\C=C/CCC(O)=O	1517.2	Standard non polar	33892256
cis-4-Decenedioic acid	OC(=O)CCCC\C=C/CCC(O)=O	1758.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
cis-4-Decenedioic acid,1TMS,isomer #1	C[Si](C)(C)OC(=O)CCCC/C=C\CCC(=O)O	1818.0	Semi standard non polar	33892256
cis-4-Decenedioic acid,1TMS,isomer #2	C[Si](C)(C)OC(=O)CC/C=C\CCCCC(=O)O	1815.9	Semi standard non polar	33892256
cis-4-Decenedioic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)CC/C=C\CCCCC(=O)O[Si](C)(C)C	1858.7	Semi standard non polar	33892256
cis-4-Decenedioic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCC/C=C\CCC(=O)O	2064.0	Semi standard non polar	33892256
cis-4-Decenedioic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CC/C=C\CCCCC(=O)O	2060.3	Semi standard non polar	33892256
cis-4-Decenedioic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC/C=C\CCCCC(=O)O[Si](C)(C)C(C)(C)C	2301.6	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 - cis-4-Decenedioic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-03du-9700000000-07830e9f3f9a840f091a	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Decenedioic acid GC-MS (2 TMS) - 70eV, Positive	splash10-024r-9350000000-da48b99466787e064f12	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Decenedioic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Decenedioic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Decenedioic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Decenedioic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Decenedioic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cis-4-Decenedioic acid GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	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 - cis-4-Decenedioic acid 10V, Positive-QTOF	splash10-0ue9-0970000000-fb6c6e0c574717d4c7c6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 20V, Positive-QTOF	splash10-0pc0-2910000000-95e303b11e1378f5fdf7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 40V, Positive-QTOF	splash10-0pdm-9200000000-15b9cbd73cfb4aa2d14e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 10V, Negative-QTOF	splash10-0002-0900000000-ca695b2f3c782ac1f498	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 20V, Negative-QTOF	splash10-052b-1900000000-1e03131c7d34ca653c8f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 40V, Negative-QTOF	splash10-0a4i-9300000000-3f7209a9d4bd721de500	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 10V, Negative-QTOF	splash10-0002-0900000000-4c0d3eb1a42e0b1c738c	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 20V, Negative-QTOF	splash10-053r-1900000000-cc2af103d9f28c259d97	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 40V, Negative-QTOF	splash10-0a4l-9300000000-cd5ea3dda94814b23400	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 10V, Positive-QTOF	splash10-0f8i-2920000000-4ebbc8b55b7ca1278acf	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 20V, Positive-QTOF	splash10-00si-9300000000-2cbdccbc7aaa465bbadd	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cis-4-Decenedioic acid 40V, Positive-QTOF	splash10-0gb9-9100000000-4e9674a449c76415b2b6	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

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 and Quantified	0 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	2380628	details
Urine	Detected and Quantified	0 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	2380628	details
Urine	Detected and Quantified	0 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	2380628	details
Urine	Detected and Quantified	0 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	2380628	details
Urine	Detected and Quantified	0 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	2380628	details
Urine	Detected and Quantified	1.129 +/- 2.259 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	2380628	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected and Quantified	1.00 (0.00-2.00) umol/mmol creatinine	Adult (>18 years old)	Both	Medium Chain Acyl-CoA Dehydrogenase Deficiency	MetaGene: Metabol...	details
Urine	Detected and Quantified	25.974 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Medium Chain Acyl-CoA Dehydrogenase Deficiency	2380628	details
Urine	Detected and Quantified	40.655 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Medium Chain Acyl-CoA Dehydrogenase Deficiency	2380628	details
Urine	Detected and Quantified	258.608 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Medium Chain Acyl-CoA Dehydrogenase Deficiency	2380628	details
Urine	Detected and Quantified	787.681 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Medium Chain Acyl-CoA Dehydrogenase Deficiency	2380628	details
Urine	Detected and Quantified	21.821-765.642 umol/mmol creatinine	Children (1-13 years old)	Not Specified	Medium Chain Acyl-CoA Dehydrogenase Deficiency	6434845	details

Associated Disorders and Diseases

Disease References

Medium Chain Acyl-CoA Dehydrogenase Deficiency

Tserng KY, Jin SJ, Kerr DS, Hoppel CL: Abnormal urinary excretion of unsaturated dicarboxylic acids in patients with medium-chain acyl-CoA dehydrogenase deficiency. J Lipid Res. 1990 May;31(5):763-71. [PubMed:2380628 ]
Duran M, De Klerk JB, Wadman SK, Bruinvis L, Ketting D: The differential diagnosis of dicarboxylic aciduria. J Inherit Metab Dis. 1984;7 Suppl 1:48-51. [PubMed:6434845 ]
G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.

Associated OMIM IDs

201450 (Medium Chain Acyl-CoA Dehydrogenase Deficiency)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022138

KNApSAcK ID

Not Available

Chemspider ID

7822621

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5578

PubChem Compound

9543671

PDB ID

Not Available

ChEBI ID

89730

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

MDB00000197

Good Scents ID

rw1896581

References

Synthesis Reference

Pourfarzam, Morteza; Bartlett, Kim. Synthesis, characterization and high-performance liquid chromatography of C6-C16 dicarboxylyl-mono-coenzyme A and -mono-carnitine esters. Journal of Chromatography (1991), 570(2), 253-76.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for cis-4-Decenedioic acid (HMDB0000603)

MOL for HMDB0000603 (cis-4-Decenedioic acid)

3D MOL for HMDB0000603 (cis-4-Decenedioic acid)

3D SDF for HMDB0000603 (cis-4-Decenedioic acid)

3D-SDF for HMDB0000603 (cis-4-Decenedioic acid)

PDB for HMDB0000603 (cis-4-Decenedioic acid)

3D PDB for HMDB0000603 (cis-4-Decenedioic acid)

SMILES for HMDB0000603 (cis-4-Decenedioic acid)

INCHI for HMDB0000603 (cis-4-Decenedioic acid)

Structure for HMDB0000603 (cis-4-Decenedioic acid)

3D Structure for HMDB0000603 (cis-4-Decenedioic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra