MiMeDB: Showing metabocard for 3-Hydroxysebacic acid (MMDBc0000512)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:39:27 UTC

Update Date

2024-04-30 19:32:43 UTC

Metabolite ID

MMDBc0000512

Metabolite Identification

Common Name

3-Hydroxysebacic acid

Description

3-Hydroxydecanedioic is a dicarboxylic acid that belongs to the class of compounds known hydroxy fatty acids. Hydroxy fatty acids are fatty acids that have hydroxyl functional groups attached to the principal chain. 3-Hydroxydecanedioic acid is found in most vertebrates. Urine from patients with ketoacidosis typically contains a number of aliphatic 3-hydroxy dicarboxylic acids, with the major compound being 3-hydroxydecanedioic acid (PMID: 7353273 ). The excretion of 3-hydroxydecanedioic acid is correlated with the excretion of hexanedioic acid, another metabolite frequently found in ketoacidosis (PMID: 5031780 ). It is thought that the 3-hydroxy dicarboxylic acids such as 3-hydroxydecanedioic acid are formed from fatty acids by a combination of omega-oxidation and incomplete beta-oxidation (PMID: 7353273 ). Marked elevation of urinary 3-hydroxydecanedioic acid has also been reported in a malnourished infant with glycogen storage disease (PMID: 8295400 ). Subsequent studies have shown that increased amounts of dicarboxylic acids, such as 3-hydroxydecanedioic acid, are typically excreted in human urine under conditions of medium-chain triglyceride (MCT) feeding, abnormal fatty acid oxidation (FAO) and fasting (PMID: 8596483 ).

Structure

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

HMDB0000350
     RDKit          3D
3-Hydroxysebacic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    5.0130    1.0438   -1.2693 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9583    0.4051   -1.4987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9162    1.0409   -2.1373 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8128   -1.0010   -1.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5182   -1.0738    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404   -0.3381    0.7025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0493   -0.9154   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1580   -0.0949    0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4210   -0.5819   -0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5455    0.3295    0.2188 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3045    1.6501   -0.1074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8797   -0.0846   -0.3466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9064    0.8245    0.1746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1078    0.6402   -0.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6532    1.8746    1.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6093    1.9654   -1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0115   -1.4801   -1.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7861   -1.5379   -1.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5410   -2.0937    0.7584 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3383   -0.5090    0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3688    0.7046    0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0282   -0.3653    1.7719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133   -1.9938    0.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1617   -0.8255   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520    0.9491    0.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2976   -0.1406    1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6524   -1.6124    0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -0.5180   -1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6237    0.2539    1.3294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6585    1.7920   -1.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334   -0.0052   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1004   -1.1475   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8081    2.8448    0.7924 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
 10 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
M  END


  Mrv1652303062020102D          

 15 14  0  0  0  0            999 V2000
   16.6711  -14.0637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5277  -15.3012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.3871  -14.8887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2421  -14.0637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.6725  -16.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.1002  -14.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8146  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3856  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.5292  -14.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6711  -14.8887    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   20.2436  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9566  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.9580  -14.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2421  -14.8887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.6725  -15.3012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 10  1  1  6  0  0  0
  2 14  1  0  0  0  0
  3 15  1  0  0  0  0
  4 14  2  0  0  0  0
  5 15  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000512

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O5/c11-8(7-10(14)15)5-3-1-2-4-6-9(12)13/h8,11H,1-7H2,(H,12,13)(H,14,15)/t8-/m1/s1

> <INCHI_KEY>
OQYZCCKCJQWHIE-MRVPVSSYSA-N

> <FORMULA>
C10H18O5

> <MOLECULAR_WEIGHT>
218.249

> <EXACT_MASS>
218.11542368

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.362731405302434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-3-hydroxydecanedioic acid

> <ALOGPS_LOGP>
0.63

> <JCHEM_LOGP>
1.0381179556666666

> <ALOGPS_LOGS>
-1.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.052863606302775

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.450063494495128

> <JCHEM_PKA_STRONGEST_BASIC>
-2.798587427000225

> <JCHEM_POLAR_SURFACE_AREA>
94.82999999999998

> <JCHEM_REFRACTIVITY>
52.658500000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.38e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-hydroxydecanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000350
     RDKit          3D
3-Hydroxysebacic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    5.0130    1.0438   -1.2693 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9583    0.4051   -1.4987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9162    1.0409   -2.1373 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8128   -1.0010   -1.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5182   -1.0738    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404   -0.3381    0.7025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0493   -0.9154   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1580   -0.0949    0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4210   -0.5819   -0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5455    0.3295    0.2188 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3045    1.6501   -0.1074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8797   -0.0846   -0.3466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9064    0.8245    0.1746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1078    0.6402   -0.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6532    1.8746    1.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6093    1.9654   -1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0115   -1.4801   -1.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7861   -1.5379   -1.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5410   -2.0937    0.7584 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3383   -0.5090    0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3688    0.7046    0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0282   -0.3653    1.7719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133   -1.9938    0.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1617   -0.8255   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520    0.9491    0.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2976   -0.1406    1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6524   -1.6124    0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -0.5180   -1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6237    0.2539    1.3294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6585    1.7920   -1.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334   -0.0052   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1004   -1.1475   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8081    2.8448    0.7924 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
 10 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
M  END

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  O   UNK     0      31.119 -26.252   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      27.118 -28.562   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      41.789 -27.792   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      28.452 -26.252   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      40.455 -30.102   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      33.787 -27.792   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      35.121 -28.562   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      32.453 -28.562   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      36.455 -27.792   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.119 -27.792   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      37.788 -28.562   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      29.786 -28.562   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      39.122 -27.792   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      28.452 -27.792   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      40.455 -28.562   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4   14                                                            
CONECT    5   15                                                            
CONECT    6    7    8                                                       
CONECT    7    6    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    1    8   12                                                  
CONECT   11    9   13                                                       
CONECT   12   10   14                                                       
CONECT   13   11   15                                                       
CONECT   14    2    4   12                                                  
CONECT   15    3    5   13                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

COMPND    HMDB0000350
HETATM    1  O1  UNL     1       5.013   1.044  -1.269  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.958   0.405  -1.499  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.916   1.041  -2.137  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.813  -1.001  -1.102  1.00  0.00           C  
HETATM    5  C3  UNL     1       3.518  -1.074   0.374  1.00  0.00           C  
HETATM    6  C4  UNL     1       2.240  -0.338   0.702  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.049  -0.915  -0.028  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.158  -0.095   0.386  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.421  -0.582  -0.287  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.546   0.329   0.219  1.00  0.00           C  
HETATM   11  O3  UNL     1      -2.305   1.650  -0.107  1.00  0.00           O  
HETATM   12  C9  UNL     1      -3.880  -0.085  -0.347  1.00  0.00           C  
HETATM   13  C10 UNL     1      -4.906   0.825   0.175  1.00  0.00           C  
HETATM   14  O4  UNL     1      -6.108   0.640  -0.187  1.00  0.00           O  
HETATM   15  O5  UNL     1      -4.653   1.875   1.038  1.00  0.00           O  
HETATM   16  H1  UNL     1       2.609   1.965  -1.854  1.00  0.00           H  
HETATM   17  H2  UNL     1       3.011  -1.480  -1.689  1.00  0.00           H  
HETATM   18  H3  UNL     1       4.786  -1.538  -1.273  1.00  0.00           H  
HETATM   19  H4  UNL     1       3.541  -2.094   0.758  1.00  0.00           H  
HETATM   20  H5  UNL     1       4.338  -0.509   0.894  1.00  0.00           H  
HETATM   21  H6  UNL     1       2.369   0.705   0.344  1.00  0.00           H  
HETATM   22  H7  UNL     1       2.028  -0.365   1.772  1.00  0.00           H  
HETATM   23  H8  UNL     1       0.913  -1.994   0.201  1.00  0.00           H  
HETATM   24  H9  UNL     1       1.162  -0.825  -1.136  1.00  0.00           H  
HETATM   25  H10 UNL     1       0.052   0.949   0.124  1.00  0.00           H  
HETATM   26  H11 UNL     1      -0.298  -0.141   1.483  1.00  0.00           H  
HETATM   27  H12 UNL     1      -1.652  -1.612   0.053  1.00  0.00           H  
HETATM   28  H13 UNL     1      -1.368  -0.518  -1.374  1.00  0.00           H  
HETATM   29  H14 UNL     1      -2.624   0.254   1.329  1.00  0.00           H  
HETATM   30  H15 UNL     1      -2.658   1.792  -1.026  1.00  0.00           H  
HETATM   31  H16 UNL     1      -3.833  -0.005  -1.451  1.00  0.00           H  
HETATM   32  H17 UNL     1      -4.100  -1.147  -0.088  1.00  0.00           H  
HETATM   33  H18 UNL     1      -4.808   2.845   0.792  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   16
CONECT    4    5   17   18
CONECT    5    6   19   20
CONECT    6    7   21   22
CONECT    7    8   23   24
CONECT    8    9   25   26
CONECT    9   10   27   28
CONECT   10   11   12   29
CONECT   11   30
CONECT   12   13   31   32
CONECT   13   14   14   15
CONECT   15   33
END

HMDB0000350
     RDKit          3D
3-Hydroxysebacic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    5.0130    1.0438   -1.2693 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9583    0.4051   -1.4987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9162    1.0409   -2.1373 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8128   -1.0010   -1.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5182   -1.0738    0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404   -0.3381    0.7025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0493   -0.9154   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1580   -0.0949    0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4210   -0.5819   -0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5455    0.3295    0.2188 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3045    1.6501   -0.1074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8797   -0.0846   -0.3466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9064    0.8245    0.1746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1078    0.6402   -0.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6532    1.8746    1.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6093    1.9654   -1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0115   -1.4801   -1.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7861   -1.5379   -1.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5410   -2.0937    0.7584 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3383   -0.5090    0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3688    0.7046    0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0282   -0.3653    1.7719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9133   -1.9938    0.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1617   -0.8255   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0520    0.9491    0.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2976   -0.1406    1.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6524   -1.6124    0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3682   -0.5180   -1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6237    0.2539    1.3294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6585    1.7920   -1.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334   -0.0052   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1004   -1.1475   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8081    2.8448    0.7924 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
 10 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  1
 11 30  1  0
 12 31  1  0
 12 32  1  0
 15 33  1  0
M  END

Synonyms

Value	Source
3-Hydroxysebacate	Generator
(R)-3-Hydroxydecanedioic acid	HMDB
(R)-3-Hydroxysebacic acid	HMDB
3-Hydroxydecanedioic acid	HMDB
3-Hydroxy-decanedioic acid	HMDB
3-Hydroxy-sebacic acid	HMDB
3-Hydroxy-decanedioate	HMDB
3-Hydroxy-sebacate	HMDB
3-Hydroxydecanedioate	HMDB
3-Hydroxysebacic acid	HMDB

Molecular Formula

C₁₀H₁₈O₅

Average Mass

218.249

Monoisotopic Mass

218.11542368

IUPAC Name

(3R)-3-hydroxydecanedioic acid

Traditional Name

(3R)-3-hydroxydecanedioic acid

CAS Registry Number

Not Available

SMILES

O[C@H](CCCCCCC(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C10H18O5/c11-8(7-10(14)15)5-3-1-2-4-6-9(12)13/h8,11H,1-7H2,(H,12,13)(H,14,15)/t8-/m1/s1

InChI Key

OQYZCCKCJQWHIE-MRVPVSSYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Medium-chain fatty acid
Hydroxy fatty acid
Beta-hydroxy acid
Fatty acyl
Fatty acid
Dicarboxylic acid or derivatives
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.38 g/L	ALOGPS
logP	0.63	ALOGPS
logP	1.04	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	4.45	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	52.66 m³·mol⁻¹	ChemAxon
Polarizability	23.36 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0159-0940000000-f4f483b1636137e43945	2020-02-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-014m-9400000000-d0cc01c70aafa53f34ab	2020-02-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00mo-9000000000-316ddd132092b08d73b4	2020-02-05	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0290000000-c2d6bda5ce3b5556855b	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-2910000000-d9a15f8576b5fb984503	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-da86659557db0db21f6b	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uxr-2970000000-01870c297f8d72ff6dc7	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0159-9200000000-b13018b3cea41f7ddcf1	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0aor-9000000000-6a2ece9abf2e1cb52c2c	2021-09-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, experimental)		2020-02-05	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, experimental)		2021-10-10	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)		2020-02-05	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0008632	3-Hydroxy-Sebacoyl Coenzyme A	3-Hydroxysebacic acid	Not Available		VMH	30371894
MMDBr0008633	3-Hydroxysebacic acid	3-Hydroxysebacic acid	Not Available		VMH	30371894
MMDBr0008634	3-Hydroxysebacic acid	3-Hydroxysebacic acid	Not Available		VMH	30371894
MMDBr0038940	3-Hydroxysebacic acid	N-(3-Hydroxydecanedioyl)-4R-hydroxysphinganine	Alkaline ceramidase YPC1	Hydrolysis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Medium chain acyl-coa dehydrogenase deficiency		Association	Human Urine	HMDB	6434845

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Bacteroidetes	1	Human feces; Human stool	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Firmicutes	1	Human	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified								HMDB
Human Urine	Detected and Quantified		10.628	308.767	umol/mmol creatinine	Children (1-13 years old)	Not Specified	Medium Chain Acyl-CoA Dehydrogenase Deficiency	HMDB	6434845
Human Urine	Detected and Quantified	5.8			umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified		0	0.6	umol/mmol creatinine	Infant (0-1 year old)	Male	Normal	HMDB	31963255
Human Urine	Detected and Quantified		0.0	0.4	umol/mmol creatinine	Infant (0-1 year old)	Female	Normal	HMDB	31963255
Human Blood	Detected and Quantified	0.65	0.32	1.2	uM	Infant (0-1 year old)	Not Specified	Normal	HMDB	2308028
Human Urine	Detected and Quantified	1.4	1.0	1.7	umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	1.9	0.1	7.0	umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	2.7	1.3	4.0	umol/mmol creatinine	Adolescent (13-18 years old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	2.9	1.7	3.8	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected and Quantified	7.7	1.5	24.1	umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	8087979
Human Urine	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0000350

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021973

KNApSAcK ID

C00052146

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

124350389

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Greter J, Lindstedt S, Seeman H, Steen G: 3-hydroxydecanedioic acid and related homologues: urinary metabolites in ketoacidosis. Clin Chem. 1980 Feb;26(2):261-5. [PubMed:7353273 ]
Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
Bergoffen J, Kaplan P, Hale DE, Bennett MJ, Berry GT: Marked elevation of urinary 3-hydroxydecanedioic acid in a malnourished infant with glycogen storage disease, mimicking long-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency. J Inherit Metab Dis. 1993;16(5):851-6. doi: 10.1007/BF00714277. [PubMed:8295400 ]
Muth A, Jung J, Bilke S, Scharrer A, Mosandl A, Sewell AC, Bohles H: Simultaneous enantioselective analysis of chiral urinary metabolites in patients with Zellweger syndrome. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 25;792(2):269-77. doi: 10.1016/s1570-0232(03)00285-x. [PubMed:12860034 ]
Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. doi: 10.1515/CCLM.2003.248. [PubMed:14708889 ]

Showing metabocard for 3-Hydroxysebacic acid (MMDBc0000512)

MOL for #<Metabolite:0x00007fd10000e078>

3D MOL for #<Metabolite:0x00007fd10000e078>

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3D-SDF for #<Metabolite:0x00007fd10000e078>

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3D PDB for #<Metabolite:0x00007fd10000e078>

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Structure for #<Metabolite:0x00007fd10000e078>

3D Structure for #<Metabolite:0x00007fd10000e078>