Jump To Section:

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

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:00:08 UTC

HMDB ID

HMDB0000350

Secondary Accession Numbers

HMDB0002534
HMDB00350
HMDB02534

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>
HMDB0000350

> <DATABASE_NAME>
hmdb

> <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

View in JSmol View NMR Assignments View Stereo Labels

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

Chemical Formula

C₁₀H₁₈O₅

Average Molecular Weight

218.249

Monoisotopic Molecular Weight

218.11542368

IUPAC Name

(3R)-3-hydroxydecanedioic acid

Traditional Name

(3R)-3-hydroxydecanedioic acid

CAS Registry Number

446881-43-2

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

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 2308028)

Excreta

Biofluid or Excreta

Urine (PMID: 8087979)
Feces (PMID: 27543620)

Source

Endogenous

Endogenous (HMDB: HMDB0000350)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Industrial application

Pharmaceutical industry

Biomarker

Medium Chain Acyl Co A Dehydrogenase Deficiency (MarkerDB: MDB00000150)

Physical Properties

State

Solid

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	151.37	30932474
DeepCCS	[M-H]-	147.63	30932474
DeepCCS	[M-2H]-	185.443	30932474
DeepCCS	[M+Na]+	161.106	30932474

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.	4.37 minutes	32390414
Predicted by Siyang on May 30, 2022	9.9348 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.89 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	177.8 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1364.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	221.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	103.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	163.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	121.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	309.9 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	351.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	244.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	712.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	297.3 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	1016.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	211.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	246.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	565.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	196.4 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	330.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Hydroxysebacic acid	O[C@H](CCCCCCC(O)=O)CC(O)=O	3075.6	Standard polar	33892256
3-Hydroxysebacic acid	O[C@H](CCCCCCC(O)=O)CC(O)=O	1693.0	Standard non polar	33892256
3-Hydroxysebacic acid	O[C@H](CCCCCCC(O)=O)CC(O)=O	1932.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Hydroxysebacic acid,1TMS,isomer #1	C[Si](C)(C)O[C@H](CCCCCCC(=O)O)CC(=O)O	1906.2	Semi standard non polar	33892256
3-Hydroxysebacic acid,1TMS,isomer #2	C[Si](C)(C)OC(=O)CCCCCC[C@@H](O)CC(=O)O	1915.3	Semi standard non polar	33892256
3-Hydroxysebacic acid,1TMS,isomer #3	C[Si](C)(C)OC(=O)C[C@H](O)CCCCCCC(=O)O	1933.8	Semi standard non polar	33892256
3-Hydroxysebacic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)CCCCCC[C@H](CC(=O)O)O[Si](C)(C)C	1964.6	Semi standard non polar	33892256
3-Hydroxysebacic acid,2TMS,isomer #2	C[Si](C)(C)OC(=O)C[C@@H](CCCCCCC(=O)O)O[Si](C)(C)C	1962.7	Semi standard non polar	33892256
3-Hydroxysebacic acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)CCCCCC[C@@H](O)CC(=O)O[Si](C)(C)C	2012.8	Semi standard non polar	33892256
3-Hydroxysebacic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)CCCCCC[C@H](CC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2071.0	Semi standard non polar	33892256
3-Hydroxysebacic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H](CCCCCCC(=O)O)CC(=O)O	2161.2	Semi standard non polar	33892256
3-Hydroxysebacic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CCCCCC[C@@H](O)CC(=O)O	2177.8	Semi standard non polar	33892256
3-Hydroxysebacic acid,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)C[C@H](O)CCCCCCC(=O)O	2172.4	Semi standard non polar	33892256
3-Hydroxysebacic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCCCC[C@H](CC(=O)O)O[Si](C)(C)C(C)(C)C	2473.2	Semi standard non polar	33892256
3-Hydroxysebacic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](CCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C	2441.4	Semi standard non polar	33892256
3-Hydroxysebacic acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)CCCCCC[C@@H](O)CC(=O)O[Si](C)(C)C(C)(C)C	2479.4	Semi standard non polar	33892256
3-Hydroxysebacic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCCCC[C@H](CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2744.0	Semi standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Blood	Detected and Quantified	0.65(0.32-1.2) uM	Infant (0-1 year old)	Not Specified	Normal	2308028	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Urine	Detected and Quantified	7.7 (1.5-24.1) umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	8087979	details
Urine	Detected and Quantified	1.9 (0.1-7.0) umol/mmol creatinine	Children (1-13 years old)	Both	Normal	8087979	details
Urine	Detected and Quantified	1.4 (1.0-1.7) umol/mmol creatinine	Children (1-13 years old)	Both	Normal	8087979	details
Urine	Detected and Quantified	2.7 (1.3-4.0) umol/mmol creatinine	Adolescent (13-18 years old)	Both	Normal	8087979	details
Urine	Detected and Quantified	5.8 umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	8087979	details
Urine	Detected and Quantified	2.9(1.7-3.8) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	0-0.6 umol/mmol creatinine	Infant (0-1 year old)	Male	Normal	31963255	details
Urine	Detected and Quantified	0.0-0.4 umol/mmol creatinine	Infant (0-1 year old)	Female	Normal	31963255	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.95-33.5 uM	Infant (0-1 year old)	Female	3-Hydroxydicarboxylic aciduria	2308028	details
Urine	Detected and Quantified	10.628-308.767 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
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 ]

Associated OMIM IDs

201450 (Medium Chain Acyl-CoA Dehydrogenase Deficiency)

External Links

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

VMH ID

Not Available

MarkerDB ID

MDB00000150

Good Scents ID

Not Available

References

Synthesis Reference

Hill, Frank Friedrich. Manufacture of 3-hydroxydicarboxylic acids. Ger. Offen. (1986), 14 pp.

Material Safety Data Sheet (MSDS)

Not Available

General References

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. [PubMed:14708889 ]
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 ]
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. [PubMed:12860034 ]
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. [PubMed:8295400 ]
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 ]

Showing metabocard for 3-Hydroxysebacic acid (HMDB0000350)

MOL for HMDB0000350 (3-Hydroxysebacic acid)

3D MOL for HMDB0000350 (3-Hydroxysebacic acid)

3D SDF for HMDB0000350 (3-Hydroxysebacic acid)

3D-SDF for HMDB0000350 (3-Hydroxysebacic acid)

PDB for HMDB0000350 (3-Hydroxysebacic acid)

3D PDB for HMDB0000350 (3-Hydroxysebacic acid)

SMILES for HMDB0000350 (3-Hydroxysebacic acid)

INCHI for HMDB0000350 (3-Hydroxysebacic acid)

Structure for HMDB0000350 (3-Hydroxysebacic acid)

3D Structure for HMDB0000350 (3-Hydroxysebacic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized