Hmdb loader

Showing metabocard for Sebacic acid (HMDB0000792)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:10 UTC
HMDB IDHMDB0000792
Secondary Accession Numbers
  • HMDB00792
Metabolite Identification
Common NameSebacic acid
DescriptionSebacic acid is a saturated, straight-chain naturally occurring dicarboxylic acid with 10 carbon atoms. Sebacic acid is a normal urinary acid. In patients with multiple acyl-CoA-dehydrogenase deficiency (MADD), also known as glutaric aciduria type II (GAII), a group of metabolic disorders due to deficiency of either electron transfer flavoprotein or electron transfer flavoprotein ubiquinone oxidoreductase, biochemical data shows an increase in urine sebacic acid excretion. Sebacic acid is found to be associated with carnitine-acylcarnitine translocase deficiency and medium chain acyl-CoA dehydrogenase deficiency, which are inborn errors of metabolism. Sebacic acid is a white flake or powdered crystal slightly soluble in water that has been proposed as an alternative energy substrate in total parenteral nutrition. Sebacic Acid was named from the Latin sebaceus (tallow candle) or sebum (tallow) in reference to its use in the manufacture of candles. Sebacic acid and its derivatives such as azelaic acid have a variety of industrial uses as plasticizers, lubricants, hydraulic fluids, cosmetics, candles, etc. It is used in the synthesis of polyamide and alkyd resins. It is also used as an intermediate for aromatics, antiseptics and painting materials (PMID: 10556649 , 1738216 , 8442769 , 12706375 ).
Structure
Data?1676999710
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000792 (Sebacic acid)

Sepiapterin.mol
  Mrv1652305271900282D          

 14 13  0  0  0  0            999 V2000
    3.2151   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2151   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9296    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9296   -0.2062    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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 11  2  0  0  0  0
  1 12  1  0  0  0  0
 10 13  2  0  0  0  0
 10 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000792 (Sebacic acid)

HMDB0000792
     RDKit          3D
Sebacic acid
 32 31  0  0  0  0  0  0  0  0999 V2000
    5.1955   -0.5268   -2.1949 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9214   -0.4396   -0.9907 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7105   -0.9664   -0.0034 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6631    0.2779   -0.5948 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6649   -0.7144   -0.0671 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3902   -0.0331    0.3420 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458    0.6116   -0.8396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5650    1.3082   -0.4653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5593    0.3298    0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8675    1.0125    0.4489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8746    0.0870    1.0330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2845   -1.0359    0.1902 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9131   -1.2930   -0.9694 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2032   -1.9298    0.7520 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4477   -0.9082    0.9679 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9988    0.9923    0.1958 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2439    0.8253   -1.4397 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0882   -1.2834    0.8012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4130   -1.4894   -0.8230 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7162   -0.7929    0.8322 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6361    0.7266    1.1306 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3907    1.2799   -1.4088 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4561   -0.2076   -1.5595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3098    2.1085    0.2609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9628    1.8167   -1.3589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1388   -0.1967    0.9816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7972   -0.4493   -0.6760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2306    1.6086   -0.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5991    1.7554    1.2581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8023    0.7103    1.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5297   -0.2419    2.0473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0448   -1.6272    1.2091 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  1  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
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  8 25  1  0
  9 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 14 32  1  0
M  END
Download

3D SDF for HMDB0000792 (Sebacic acid)

Sepiapterin.mol
  Mrv1652305271900282D          

 14 13  0  0  0  0            999 V2000
    3.2151   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2151   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9296    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9296   -0.2062    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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 11  2  0  0  0  0
  1 12  1  0  0  0  0
 10 13  2  0  0  0  0
 10 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000792

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CCCCCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1-8H2,(H,11,12)(H,13,14)

> <INCHI_KEY>
CXMXRPHRNRROMY-UHFFFAOYSA-N

> <FORMULA>
C10H18O4

> <MOLECULAR_WEIGHT>
202.2475

> <EXACT_MASS>
202.120509064

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
22.611318956480364

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
decanedioic acid

> <ALOGPS_LOGP>
1.93

> <JCHEM_LOGP>
2.2689290226666663

> <ALOGPS_LOGS>
-2.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.322146872710726

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.720086881382763

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
51.143

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.12e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sebacic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000792 (Sebacic acid)

HMDB0000792
     RDKit          3D
Sebacic acid
 32 31  0  0  0  0  0  0  0  0999 V2000
    5.1955   -0.5268   -2.1949 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9214   -0.4396   -0.9907 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7105   -0.9664   -0.0034 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6631    0.2779   -0.5948 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6649   -0.7144   -0.0671 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3902   -0.0331    0.3420 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458    0.6116   -0.8396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5650    1.3082   -0.4653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5593    0.3298    0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8675    1.0125    0.4489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8746    0.0870    1.0330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2845   -1.0359    0.1902 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9131   -1.2930   -0.9694 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2032   -1.9298    0.7520 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4477   -0.9082    0.9679 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9988    0.9923    0.1958 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2439    0.8253   -1.4397 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0882   -1.2834    0.8012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4130   -1.4894   -0.8230 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7162   -0.7929    0.8322 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6361    0.7266    1.1306 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3907    1.2799   -1.4088 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4561   -0.2076   -1.5595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3098    2.1085    0.2609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9628    1.8167   -1.3589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1388   -0.1967    0.9816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7972   -0.4493   -0.6760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2306    1.6086   -0.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5991    1.7554    1.2581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8023    0.7103    1.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5297   -0.2419    2.0473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0448   -1.6272    1.2091 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  1  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
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  8 25  1  0
  9 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 14 32  1  0
M  END
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PDB for HMDB0000792 (Sebacic acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Sepiapterin.mol                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       6.002  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.668   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.334  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.001   0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.667   0.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.001  -0.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.334   0.385   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.668  -0.385   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.002   0.385   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       6.002  -1.925   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       7.335   0.385   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -6.002   1.925   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -7.335  -0.385   0.000  0.00  0.00           O+0
CONECT    1    2   11   12                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   13   14                                                  
CONECT   11    1                                                            
CONECT   12    1                                                            
CONECT   13   10                                                            
CONECT   14   10                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for HMDB0000792 (Sebacic acid)

COMPND    HMDB0000792
HETATM    1  O1  UNL     1       5.196  -0.527  -2.195  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.921  -0.440  -0.991  1.00  0.00           C  
HETATM    3  O2  UNL     1       5.711  -0.966  -0.003  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.663   0.278  -0.595  1.00  0.00           C  
HETATM    5  C3  UNL     1       2.665  -0.714  -0.067  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.390  -0.033   0.342  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.746   0.612  -0.840  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.565   1.308  -0.465  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.559   0.330   0.102  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.867   1.013   0.449  1.00  0.00           C  
HETATM   11  C9  UNL     1      -3.875   0.087   1.033  1.00  0.00           C  
HETATM   12  C10 UNL     1      -4.285  -1.036   0.190  1.00  0.00           C  
HETATM   13  O3  UNL     1      -3.913  -1.293  -0.969  1.00  0.00           O  
HETATM   14  O4  UNL     1      -5.203  -1.930   0.752  1.00  0.00           O  
HETATM   15  H1  UNL     1       5.448  -0.908   0.968  1.00  0.00           H  
HETATM   16  H2  UNL     1       3.999   0.992   0.196  1.00  0.00           H  
HETATM   17  H3  UNL     1       3.244   0.825  -1.440  1.00  0.00           H  
HETATM   18  H4  UNL     1       3.088  -1.283   0.801  1.00  0.00           H  
HETATM   19  H5  UNL     1       2.413  -1.489  -0.823  1.00  0.00           H  
HETATM   20  H6  UNL     1       0.716  -0.793   0.832  1.00  0.00           H  
HETATM   21  H7  UNL     1       1.636   0.727   1.131  1.00  0.00           H  
HETATM   22  H8  UNL     1       1.391   1.280  -1.409  1.00  0.00           H  
HETATM   23  H9  UNL     1       0.456  -0.208  -1.560  1.00  0.00           H  
HETATM   24  H10 UNL     1      -0.310   2.109   0.261  1.00  0.00           H  
HETATM   25  H11 UNL     1      -0.963   1.817  -1.359  1.00  0.00           H  
HETATM   26  H12 UNL     1      -1.139  -0.197   0.982  1.00  0.00           H  
HETATM   27  H13 UNL     1      -1.797  -0.449  -0.676  1.00  0.00           H  
HETATM   28  H14 UNL     1      -3.231   1.609  -0.391  1.00  0.00           H  
HETATM   29  H15 UNL     1      -2.599   1.755   1.258  1.00  0.00           H  
HETATM   30  H16 UNL     1      -4.802   0.710   1.230  1.00  0.00           H  
HETATM   31  H17 UNL     1      -3.530  -0.242   2.047  1.00  0.00           H  
HETATM   32  H18 UNL     1      -6.045  -1.627   1.209  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   20   21
CONECT    7    8   22   23
CONECT    8    9   24   25
CONECT    9   10   26   27
CONECT   10   11   28   29
CONECT   11   12   30   31
CONECT   12   13   13   14
CONECT   14   32
END
Download

SMILES for HMDB0000792 (Sebacic acid)

OC(=O)CCCCCCCCC(O)=O
Download

INCHI for HMDB0000792 (Sebacic acid)

InChI=1S/C10H18O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1-8H2,(H,11,12)(H,13,14)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,10-Decanedioic acidChEBI
1,8-DicarboxyoctaneChEBI
Decanedioic acidChEBI
SebacinsaeureChEBI
1,10-DecanedioateGenerator
DecanedioateGenerator
SebacateGenerator
1,8-OctanedicarboxylateHMDB
1,8-Octanedicarboxylic acidHMDB
4,7-Dioxosebacic acidHMDB
4-OxodecanedioateHMDB
4-Oxodecanedioic acidHMDB
Acide sebaciqueHMDB
Decanedicarboxylic acidHMDB
Dicarboxylic acid C10HMDB
Ipomic acidHMDB
N-DecanedioateHMDB
N-Decanedioic acidHMDB
Sebacic acidsHMDB
SebacinsaureHMDB
Seracic acidHMDB
Sebacic acid, aluminum saltHMDB
Sebacic acid, monocadmium saltHMDB
Sebacic acid, sodium saltHMDB
Chemical FormulaC10H18O4
Average Molecular Weight202.2475
Monoisotopic Molecular Weight202.120509064
IUPAC Namedecanedioic acid
Traditional Namesebacic acid
CAS Registry Number111-20-6
SMILES
OC(=O)CCCCCCCCC(O)=O
InChI Identifier
InChI=1S/C10H18O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1-8H2,(H,11,12)(H,13,14)
InChI KeyCXMXRPHRNRROMY-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain 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 FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point130.8 °CNot Available
Boiling Point364.00 to 365.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1 mg/mLNot Available
LogP1.706 (est)The Good Scents Company Information System
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg141.89630932474
[M-H]-Not Available143.6http://allccs.zhulab.cn/database/detail?ID=AllCCS00000215
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.91 g/LALOGPS
logP1.93ALOGPS
logP2.27ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)4.72ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity51.14 m³·mol⁻¹ChemAxon
Polarizability22.61 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+149.39531661259
DarkChem[M-H]-145.43431661259
AllCCS[M+H]+146.47732859911
AllCCS[M-H]-148.44732859911
DeepCCS[M+H]+145.88830932474
DeepCCS[M-H]-142.06130932474
DeepCCS[M-2H]-179.20730932474
DeepCCS[M+Na]+154.87230932474
AllCCS[M+H]+146.532859911
AllCCS[M+H-H2O]+142.932859911
AllCCS[M+NH4]+149.832859911
AllCCS[M+Na]+150.832859911
AllCCS[M-H]-148.432859911
AllCCS[M+Na-2H]-149.632859911
AllCCS[M+HCOO]-150.932859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.5.73 minutes32390414
Predicted by Siyang on May 30, 202211.0731 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.23 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid47.3 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1826.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid288.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid137.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid182.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid300.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid395.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid446.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)122.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid966.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid368.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1136.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid312.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid313.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate437.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA240.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water246.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Sebacic acidOC(=O)CCCCCCCCC(O)=O2685.7Standard polar33892256
Sebacic acidOC(=O)CCCCCCCCC(O)=O1579.5Standard non polar33892256
Sebacic acidOC(=O)CCCCCCCCC(O)=O1772.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Sebacic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)CCCCCCCCC(=O)O1813.8Semi standard non polar33892256
Sebacic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)CCCCCCCCC(=O)O[Si](C)(C)C1909.9Semi standard non polar33892256
Sebacic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCCCCCCC(=O)O2060.3Semi standard non polar33892256
Sebacic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCCCCCCCC(=O)O[Si](C)(C)C(C)(C)C2389.3Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
BloodDetected and Quantified0.091(0.072-0.11) uMInfant (0-1 year old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
FecesDetected and Quantified11.0755 +/- 10.235 nmol/g wet fecesNot SpecifiedNot Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal		 details
UrineDetected and Quantified0-0.8 umol/mmol creatinineInfant (0-1 year old)Male
Normal		 details
UrineDetected and Quantified0-1.0 umol/mmol creatinineInfant (0-1 year old)Male
Normal		 details
UrineDetected and Quantified0-1.8 umol/mmol creatinineInfant (0-1 year old)Female
Normal		 details
UrineDetected and Quantified<8 umol/mmol creatinineNot SpecifiedNot SpecifiedNormal details
UrineDetected and Quantified9.503 +/- 12.857 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal		 details
UrineDetected and Quantified4.472 +/- 3.913 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal		 details
UrineDetected and Quantified1.118 +/- 2.795 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal		 details
UrineDetected and Quantified1-4 umol/mmol creatinineChildren (1 - 13 years old)BothNormal details
UrineDetected and Quantified0 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal		 details
UrineDetected and Quantified2.0 - 5.0 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
UrineDetected and Quantified0 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal		 details
UrineDetected and Quantified<9.83 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
 details
UrineDetected and Quantified4.493 +/- 2.271 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Analysis of 30 no...
 details
UrineDetected and Quantified3.565 +/- 3.385 umol/mmol creatinineAdult (>18 years old)BothNot Available details
UrineDetected and Quantified1.9 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified9.5 +/- 12.8 umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected and Quantified0.60 +/- 0.78 umol/mmol creatinineInfant (0-1 year old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.70-3.7 uMInfant (0-1 year old)Female3-Hydroxydicarboxylic aciduria details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothIron deficiency details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothUlcerative colitis details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
UrineDetected and Quantified50.312 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Medium Chain Acyl-CoA Dehydrogenase Deficiency		 details
UrineDetected and Quantified1 umol/mmol creatinineInfant (0-1 year old)Male3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency details
UrineDetected and Quantified57-266 umol/mmol creatinineNewborn (0-30 days old)BothCarnitine-acylcarnitine translocase deficiency details
UrineDetected and Quantified94 umol/mmol creatinineNewborn (0-30 days old)Not Specified
Carnitine-acylcarnitine translocase deficiency		 details
UrineDetected and Quantified3-112 umol/mmol creatinineChildren (1 - 13 years old)BothMedium Chain Acyl-CoA Dehydrogenase Deficiency details
UrineDetected and Quantified527.713 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Medium Chain Acyl-CoA Dehydrogenase Deficiency		 details
UrineDetected and Quantified275.596 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Medium Chain Acyl-CoA Dehydrogenase Deficiency		 details
UrineDetected and Quantified1.0 (0.0-2.0) umol/mmol creatinineAdult (>18 years old)BothCarnitine-acylcarnitine translocase deficiency
    • MetaGene: Metabol...
 details
UrineDetected and Quantified0 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Medium Chain Acyl-CoA Dehydrogenase Deficiency		 details
UrineDetected and Quantified0 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Medium Chain Acyl-CoA Dehydrogenase Deficiency		 details
UrineDetected and Quantified9.263 +/- 8.411 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 details
UrineDetected and Quantified161.5 (57.0-266.0) umol/mmol creatinineChildren (1-13 years old)BothCarnitine-Acylcarnitine translocase deficiency
    • MetaGene: Metabol...
 details
Associated Disorders and Diseases
Disease References
3-Hydroxydicarboxylic aciduria
  1. Hagenfeldt L, von Dobeln U, Holme E, Alm J, Brandberg G, Enocksson E, Lindeberg L: 3-Hydroxydicarboxylic aciduria--a fatty acid oxidation defect with severe prognosis. J Pediatr. 1990 Mar;116(3):387-92. [PubMed:2308028 ]
Iron deficiency
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Ulcerative colitis
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
  2. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  3. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Carnitine-acylcarnitine translocase deficiency
  1. Stanley CA, Hale DE, Berry GT, Deleeuw S, Boxer J, Bonnefont JP: Brief report: a deficiency of carnitine-acylcarnitine translocase in the inner mitochondrial membrane. N Engl J Med. 1992 Jul 2;327(1):19-23. [PubMed:1598097 ]
  2. Ogier de Baulny H, Slama A, Touati G, Turnbull DM, Pourfarzam M, Brivet M: Neonatal hyperammonemia caused by a defect of carnitine-acylcarnitine translocase. J Pediatr. 1995 Nov;127(5):723-8. [PubMed:7472823 ]
  3. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Medium Chain Acyl-CoA Dehydrogenase Deficiency
  1. 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 ]
  2. Gregersen N, Kolvraa S, Rasmussen K, Mortensen PB, Divry P, David M, Hobolth N: General (medium-chain) acyl-CoA dehydrogenase deficiency (non-ketotic dicarboxylic aciduria): quantitative urinary excretion pattern of 23 biologically significant organic acids in three cases. Clin Chim Acta. 1983 Aug 15;132(2):181-91. [PubMed:6616873 ]
3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency
  1. Conboy E, Vairo F, Schultz M, Agre K, Ridsdale R, Deyle D, Oglesbee D, Gavrilov D, Klee EW, Lanpher B: Mitochondrial 3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency: Unique Presenting Laboratory Values and a Review of Biochemical and Clinical Features. JIMD Rep. 2017 Oct 14. doi: 10.1007/8904_2017_59. [PubMed:29030856 ]
Associated OMIM IDs
  • 114500 (Colorectal cancer)
  • 212138 (Carnitine-acylcarnitine translocase deficiency)
  • 610247 (Eosinophilic esophagitis)
  • 201450 (Medium Chain Acyl-CoA Dehydrogenase Deficiency)
  • 605911 (3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency)
DrugBank IDDB07645
Phenol Explorer Compound IDNot Available
FooDB IDFDB022247
KNApSAcK IDC00001202
Chemspider ID5004
KEGG Compound IDC08277
BioCyc IDCPD-3623
BiGG IDNot Available
Wikipedia LinkSebacic_acid
METLIN ID4240
PubChem Compound5192
PDB IDNot Available
ChEBI ID41865
Food Biomarker OntologyNot Available
VMH IDSEBACID
MarkerDB IDMDB00000254
Good Scents IDrw1281881
References
Synthesis ReferenceLi, Aimin; Jiang, Zhenmao; Cai, Jianguo; Zhang, Xiao; Shi, Hongyan; Zhou, Jiayan; Zhang, Quanxing; Long, Chao; Liu, Fuqiang; Chen, Jinlong. Environmental friendly method for producing sebacic acid using anion exchangers and polymer adsorbents. Faming Zhuanli Shenqing Gongkai Shuomingshu (2005), 5 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38. [PubMed:2026685 ]
  2. Jakobs C, Sweetman L, Wadman SK, Duran M, Saudubray JM, Nyhan WL: Prenatal diagnosis of glutaric aciduria type II by direct chemical analysis of dicarboxylic acids in amniotic fluid. Eur J Pediatr. 1984 Jan;141(3):153-7. [PubMed:6698061 ]
  3. Fleming AB, Saltzman WM: Pharmacokinetics of the carmustine implant. Clin Pharmacokinet. 2002;41(6):403-19. [PubMed:12074689 ]
  4. Gregersen N, Kolvraa S, Mortensen PB, Rasmussen K: C6-C10-dicarboxylic aciduria: biochemical considerations in relation to diagnosis of beta-oxidation defects. Scand J Clin Lab Invest Suppl. 1982;161:15-27. [PubMed:6959231 ]
  5. Bertuzzi A, Finotti E, Mingrone G, Greco AV: Sebacic acid binding to human plasma albumin. Biochem Pharmacol. 1993 Feb 9;45(3):697-702. [PubMed:8442769 ]
  6. Capristo E, Mingrone G, De Gaetano A, Addolorato G, Greco AV, Gasbarrini G: A new HPLC method for the direct analysis of triglycerides of dicarboxylic acids in biological samples. Clin Chim Acta. 1999 Nov;289(1-2):11-21. [PubMed:10556649 ]
  7. Mingrone G, Tacchino RM, Castagneto M, Finotti E, Greco AV: Use of even-numbered carbon atom dicarboxylic salts in parenteral nutrition as fuel substrate. JPEN J Parenter Enteral Nutr. 1992 Jan-Feb;16(1):32-8. [PubMed:1738216 ]
  8. Curcoy A, Olsen RK, Ribes A, Trenchs V, Vilaseca MA, Campistol J, Osorio JH, Andresen BS, Gregersen N: Late-onset form of beta-electron transfer flavoprotein deficiency. Mol Genet Metab. 2003 Apr;78(4):247-9. [PubMed:12706375 ]