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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2022-03-07 02:49:02 UTC

HMDB ID

HMDB0000413

Secondary Accession Numbers

HMDB00413

Metabolite Identification

Common Name

3-Hydroxydodecanedioic acid

Description

3-Hydroxydodecanedioic acid 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. In humans, 3-hydroxydodecanedioic acid is involved in the acylcarnitine 3-hydroxydodecanedioylcarnitine pathway. 3-Hydroxydodecanedioic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 3-hydroxydodecanedioic acid a potential biomarker for the consumption of these foods. 3-Hydroxydodecanedioic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a small amount of articles have been published on 3-Hydroxydodecanedioic acid.

Structure

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

HMDB0000413
     RDKit          3D
3-Hydroxydodecanedioic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.4071   -2.1119   -0.8516 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6775   -0.8959   -0.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4151   -0.3136   -1.7863 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2361   -0.1100    0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8715    0.4784    0.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9071   -0.6346   -0.0976 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4984   -0.1590   -0.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9881    0.6073    0.7839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4104    1.0880    0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184   -0.0658    0.2665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7439    0.4733    0.0049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5888   -0.7594   -0.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5172   -1.5422    0.9333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9878   -0.4594   -0.6305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7504    0.3216    0.3432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2386    0.6787    1.4253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0626    0.6724    0.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8525    0.5915   -1.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1959   -0.7354    1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9848    0.6996    0.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9417    1.0877   -0.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5841    1.1570    0.9854 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2729   -1.2672   -0.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8337   -1.2366    0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5387    0.4340   -1.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8948   -1.0685   -0.6072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9804   -0.0429    1.7005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6333    1.4702    1.0602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299    1.6795    1.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4450    1.7320   -0.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0402   -0.6827   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4090   -0.7032    1.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7368    1.1413   -0.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9992    1.0084    0.9413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0830   -1.3277   -1.0341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4754   -0.9497    1.7319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4856   -1.4228   -0.8710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9282    0.0844   -1.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6631    1.0829    0.7842 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  1  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 17 39  1  0
M  END

3-Hydroxydodecanedioic acid.mol
  Mrv1652305261923572D          

 17 16  0  0  0  0            999 V2000
    3.2151    1.0312    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
    2.5006   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9296    1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9296   -1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862    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
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  1 13  2  0  0  0  0
  1 14  1  0  0  0  0
 12 15  2  0  0  0  0
 12 16  1  0  0  0  0
  3 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000413

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H22O5/c13-10(9-12(16)17)7-5-3-1-2-4-6-8-11(14)15/h10,13H,1-9H2,(H,14,15)(H,16,17)

> <INCHI_KEY>
FYVQCLGZFXHEGL-UHFFFAOYSA-N

> <FORMULA>
C12H22O5

> <MOLECULAR_WEIGHT>
246.3001

> <EXACT_MASS>
246.146723814

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
27.581064277535233

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxydodecanedioic acid

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
1.9272552856666674

> <ALOGPS_LOGS>
-2.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.135176336436662

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.488693485812775

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7985874263187887

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
61.8605

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxydodecanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000413
     RDKit          3D
3-Hydroxydodecanedioic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.4071   -2.1119   -0.8516 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6775   -0.8959   -0.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4151   -0.3136   -1.7863 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2361   -0.1100    0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8715    0.4784    0.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9071   -0.6346   -0.0976 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4984   -0.1590   -0.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9881    0.6073    0.7839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4104    1.0880    0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184   -0.0658    0.2665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7439    0.4733    0.0049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5888   -0.7594   -0.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5172   -1.5422    0.9333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9878   -0.4594   -0.6305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7504    0.3216    0.3432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2386    0.6787    1.4253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0626    0.6724    0.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8525    0.5915   -1.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1959   -0.7354    1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9848    0.6996    0.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9417    1.0877   -0.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5841    1.1570    0.9854 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2729   -1.2672   -0.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8337   -1.2366    0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5387    0.4340   -1.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8948   -1.0685   -0.6072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9804   -0.0429    1.7005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6333    1.4702    1.0602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299    1.6795    1.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4450    1.7320   -0.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0402   -0.6827   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4090   -0.7032    1.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7368    1.1413   -0.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9992    1.0084    0.9413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0830   -1.3277   -1.0341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4754   -0.9497    1.7319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4856   -1.4228   -0.8710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9282    0.0844   -1.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6631    1.0829    0.7842 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  1  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 17 39  1  0
M  END

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Hydroxydodecanedioic acid.mol                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       6.002   1.925   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.002   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.668  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.668  -1.925   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.334  -2.695   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.001  -1.925   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.667  -2.695   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.667  -1.925   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.001  -2.695   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.334  -1.925   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.668  -2.695   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.002  -1.925   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.668   2.695   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       7.335   2.695   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -6.002  -0.385   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -7.335  -2.695   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.334   0.385   0.000  0.00  0.00           O+0
CONECT    1    2   13   14                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   17                                                  
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   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   15   16                                                  
CONECT   13    1                                                            
CONECT   14    1                                                            
CONECT   15   12                                                            
CONECT   16   12                                                            
CONECT   17    3                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

COMPND    HMDB0000413
HETATM    1  O1  UNL     1       5.407  -2.112  -0.852  1.00  0.00           O  
HETATM    2  C1  UNL     1       5.678  -0.896  -0.747  1.00  0.00           C  
HETATM    3  O2  UNL     1       6.415  -0.314  -1.786  1.00  0.00           O  
HETATM    4  C2  UNL     1       5.236  -0.110   0.425  1.00  0.00           C  
HETATM    5  C3  UNL     1       3.871   0.478   0.152  1.00  0.00           C  
HETATM    6  C4  UNL     1       2.907  -0.635  -0.098  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.498  -0.159  -0.387  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.988   0.607   0.784  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.410   1.088   0.506  1.00  0.00           C  
HETATM   10  C8  UNL     1      -1.318  -0.066   0.267  1.00  0.00           C  
HETATM   11  C9  UNL     1      -2.744   0.473   0.005  1.00  0.00           C  
HETATM   12  C10 UNL     1      -3.589  -0.759  -0.225  1.00  0.00           C  
HETATM   13  O3  UNL     1      -3.517  -1.542   0.933  1.00  0.00           O  
HETATM   14  C11 UNL     1      -4.988  -0.459  -0.630  1.00  0.00           C  
HETATM   15  C12 UNL     1      -5.750   0.322   0.343  1.00  0.00           C  
HETATM   16  O4  UNL     1      -5.239   0.679   1.425  1.00  0.00           O  
HETATM   17  O5  UNL     1      -7.063   0.672   0.063  1.00  0.00           O  
HETATM   18  H1  UNL     1       6.853   0.592  -1.594  1.00  0.00           H  
HETATM   19  H2  UNL     1       5.196  -0.735   1.346  1.00  0.00           H  
HETATM   20  H3  UNL     1       5.985   0.700   0.649  1.00  0.00           H  
HETATM   21  H4  UNL     1       3.942   1.088  -0.773  1.00  0.00           H  
HETATM   22  H5  UNL     1       3.584   1.157   0.985  1.00  0.00           H  
HETATM   23  H6  UNL     1       3.273  -1.267  -0.940  1.00  0.00           H  
HETATM   24  H7  UNL     1       2.834  -1.237   0.853  1.00  0.00           H  
HETATM   25  H8  UNL     1       1.539   0.434  -1.321  1.00  0.00           H  
HETATM   26  H9  UNL     1       0.895  -1.068  -0.607  1.00  0.00           H  
HETATM   27  H10 UNL     1       0.980  -0.043   1.701  1.00  0.00           H  
HETATM   28  H11 UNL     1       1.633   1.470   1.060  1.00  0.00           H  
HETATM   29  H12 UNL     1      -0.830   1.680   1.346  1.00  0.00           H  
HETATM   30  H13 UNL     1      -0.445   1.732  -0.412  1.00  0.00           H  
HETATM   31  H14 UNL     1      -1.040  -0.683  -0.629  1.00  0.00           H  
HETATM   32  H15 UNL     1      -1.409  -0.703   1.159  1.00  0.00           H  
HETATM   33  H16 UNL     1      -2.737   1.141  -0.876  1.00  0.00           H  
HETATM   34  H17 UNL     1      -2.999   1.008   0.941  1.00  0.00           H  
HETATM   35  H18 UNL     1      -3.083  -1.328  -1.034  1.00  0.00           H  
HETATM   36  H19 UNL     1      -3.475  -0.950   1.732  1.00  0.00           H  
HETATM   37  H20 UNL     1      -5.486  -1.423  -0.871  1.00  0.00           H  
HETATM   38  H21 UNL     1      -4.928   0.084  -1.617  1.00  0.00           H  
HETATM   39  H22 UNL     1      -7.663   1.083   0.784  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7   23   24
CONECT    7    8   25   26
CONECT    8    9   27   28
CONECT    9   10   29   30
CONECT   10   11   31   32
CONECT   11   12   33   34
CONECT   12   13   14   35
CONECT   13   36
CONECT   14   15   37   38
CONECT   15   16   16   17
CONECT   17   39
END

HMDB0000413
     RDKit          3D
3-Hydroxydodecanedioic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.4071   -2.1119   -0.8516 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6775   -0.8959   -0.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4151   -0.3136   -1.7863 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2361   -0.1100    0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8715    0.4784    0.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9071   -0.6346   -0.0976 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4984   -0.1590   -0.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9881    0.6073    0.7839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4104    1.0880    0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184   -0.0658    0.2665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7439    0.4733    0.0049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5888   -0.7594   -0.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5172   -1.5422    0.9333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9878   -0.4594   -0.6305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7504    0.3216    0.3432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2386    0.6787    1.4253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0626    0.6724    0.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8525    0.5915   -1.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1959   -0.7354    1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9848    0.6996    0.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9417    1.0877   -0.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5841    1.1570    0.9854 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2729   -1.2672   -0.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8337   -1.2366    0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5387    0.4340   -1.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8948   -1.0685   -0.6072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9804   -0.0429    1.7005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6333    1.4702    1.0602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299    1.6795    1.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4450    1.7320   -0.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0402   -0.6827   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4090   -0.7032    1.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7368    1.1413   -0.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9992    1.0084    0.9413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0830   -1.3277   -1.0341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4754   -0.9497    1.7319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4856   -1.4228   -0.8710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9282    0.0844   -1.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6631    1.0829    0.7842 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  1  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 17 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Hydroxydodecanedioate	Generator
3-Hydroxy-dodecanedioate	HMDB

Chemical Formula

C₁₂H₂₂O₅

Average Molecular Weight

246.3001

Monoisotopic Molecular Weight

246.146723814

IUPAC Name

3-hydroxydodecanedioic acid

Traditional Name

3-hydroxydodecanedioic acid

CAS Registry Number

34574-69-1

SMILES

OC(CCCCCCCCC(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C12H22O5/c13-10(9-12(16)17)7-5-3-1-2-4-6-8-11(14)15/h10,13H,1-9H2,(H,14,15)(H,16,17)

InChI Key

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Dicarboxylic acids (LMFA01170089 )

Ontology

Not Available

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	0.83 g/L	ALOGPS
logP	1.49	ALOGPS
logP	1.93	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	4.49	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	11	ChemAxon
Refractivity	61.86 m³·mol⁻¹	ChemAxon
Polarizability	27.58 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	160.897	31661259
DarkChem	[M-H]-	155.565	31661259
AllCCS	[M+H]+	158.488	32859911
AllCCS	[M-H]-	159.625	32859911
DeepCCS	[M+H]+	157.192	30932474
DeepCCS	[M-H]-	153.169	30932474
DeepCCS	[M-2H]-	190.997	30932474
DeepCCS	[M+Na]+	166.661	30932474
AllCCS	[M+H]+	158.5	32859911
AllCCS	[M+H-H2O]+	155.2	32859911
AllCCS	[M+NH4]+	161.5	32859911
AllCCS	[M+Na]+	162.4	32859911
AllCCS	[M-H]-	159.6	32859911
AllCCS	[M+Na-2H]-	160.4	32859911
AllCCS	[M+HCOO]-	161.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Hydroxydodecanedioic acid	OC(CCCCCCCCC(O)=O)CC(O)=O	3328.0	Standard polar	33892256
3-Hydroxydodecanedioic acid	OC(CCCCCCCCC(O)=O)CC(O)=O	1793.1	Standard non polar	33892256
3-Hydroxydodecanedioic acid	OC(CCCCCCCCC(O)=O)CC(O)=O	2100.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Hydroxydodecanedioic acid,1TMS,isomer #1	C[Si](C)(C)OC(CCCCCCCCC(=O)O)CC(=O)O	2137.6	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,1TMS,isomer #2	C[Si](C)(C)OC(=O)CCCCCCCCC(O)CC(=O)O	2164.0	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,1TMS,isomer #3	C[Si](C)(C)OC(=O)CC(O)CCCCCCCCC(=O)O	2156.4	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)CCCCCCCCC(CC(=O)O)O[Si](C)(C)C	2201.3	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,2TMS,isomer #2	C[Si](C)(C)OC(=O)CC(CCCCCCCCC(=O)O)O[Si](C)(C)C	2180.9	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)CCCCCCCCC(O)CC(=O)O[Si](C)(C)C	2231.1	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)CCCCCCCCC(CC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2257.8	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(CCCCCCCCC(=O)O)CC(=O)O	2402.8	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CCCCCCCCC(O)CC(=O)O	2421.0	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)CC(O)CCCCCCCCC(=O)O	2407.8	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCCCCCCC(CC(=O)O)O[Si](C)(C)C(C)(C)C	2719.5	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CC(CCCCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C	2680.6	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)CCCCCCCCC(O)CC(=O)O[Si](C)(C)C(C)(C)C	2704.7	Semi standard non polar	33892256
3-Hydroxydodecanedioic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCCCCCCC(CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2934.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9840000000-ba1d51f5769b6001dfc1	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (3 TMS) - 70eV, Positive	splash10-009t-6339200000-6b8f2d46e5131baa2bf8	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxydodecanedioic acid GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 10V, Positive-QTOF	splash10-01t9-0190000000-56a5ca0692bd052ae94f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 20V, Positive-QTOF	splash10-02e9-1960000000-e2b23bf3215485b28bba	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 40V, Positive-QTOF	splash10-029y-9800000000-cdbf0382e047c2655d99	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 10V, Negative-QTOF	splash10-002b-0190000000-659140900506a85c6c83	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 20V, Negative-QTOF	splash10-0kea-0590000000-30d125dca29237080fb2	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 40V, Negative-QTOF	splash10-0a4l-9610000000-9f27770ca089c740fe35	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 10V, Positive-QTOF	splash10-004j-2790000000-8872855000b5f36f50f4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 20V, Positive-QTOF	splash10-07r9-9510000000-6ac3800480ad36de5364	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 40V, Positive-QTOF	splash10-0a4i-9100000000-e2e1e808d7a4b61debb4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 10V, Negative-QTOF	splash10-002b-0090000000-2cc995a8b8c0ea7aebd1	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 20V, Negative-QTOF	splash10-0a4j-5490000000-60cdf4bc23e2a4a49cf0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxydodecanedioic acid 40V, Negative-QTOF	splash10-0a4i-9410000000-7e8cf4471e074c5cf421	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2012-12-04	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.61(0.39-1.1) uM	Infant (0-1 year old)	Not Specified	Normal	2308028	details
Urine	Detected and Quantified	0 umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	1870421	details
Urine	Detected and Quantified	0.918 +/- 1.836 umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	1870421	details
Urine	Detected and Quantified	3.672 +/- 3.213 umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	1870421	details
Urine	Detected and Quantified	9.181 +/- 3.672 umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	1870421	details
Urine	Detected and Quantified	20.657 +/- 15.148 umol/mmol creatinine	Children (1-13 years old)	Not Specified	Normal	1870421	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.79-19.2 uM uM	Infant (0-1 year old)	Female	3-Hydroxydicarboxylic aciduria	2308028	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	ovarian cancer	26573008	details
Urine	Detected and Quantified	37.182-550.840 umol/mmol creatinine	Infant (0-1 year old)	Not Specified	3-Hydroxydicarboxylic aciduria	1870421	details

Associated Disorders and Diseases

Disease References

Ovarian cancer
Gaul DA, Mezencev R, Long TQ, Jones CM, Benigno BB, Gray A, Fernandez FM, McDonald JF: Highly-accurate metabolomic detection of early-stage ovarian cancer. Sci Rep. 2015 Nov 17;5:16351. doi: 10.1038/srep16351. [PubMed:26573008 ]
3-Hydroxydicarboxylic aciduria
Tserng KY, Jin SJ, Kerr DS, Hoppel CL: Urinary 3-hydroxydicarboxylic acids in pathophysiology of metabolic disorders with dicarboxylic aciduria. Metabolism. 1991 Jul;40(7):676-82. [PubMed:1870421 ]

Associated OMIM IDs

167000 (Ovarian cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022029

KNApSAcK ID

Not Available

Chemspider ID

13628081

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5402

PubChem Compound

16663321

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Schreurs, P. H. M.; Montijn, P. P.; Hoff, S. New synthesis of trans-2-dodecene-1,12-dioic acid (traumatic acid). Recueil des Travaux Chimiques des Pays-Bas (1971), 90(12), 1331-2.

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 ]
Korman SH, Mandel H, Gutman A: Characteristic urine organic acid profile in peroxisomal biogenesis disorders. J Inherit Metab Dis. 2000 Jun;23(4):425-8. [PubMed:10896310 ]

Showing metabocard for 3-Hydroxydodecanedioic acid (HMDB0000413)

MOL for HMDB0000413 (3-Hydroxydodecanedioic acid)

3D MOL for HMDB0000413 (3-Hydroxydodecanedioic acid)

3D SDF for HMDB0000413 (3-Hydroxydodecanedioic acid)

3D-SDF for HMDB0000413 (3-Hydroxydodecanedioic acid)

PDB for HMDB0000413 (3-Hydroxydodecanedioic acid)

3D PDB for HMDB0000413 (3-Hydroxydodecanedioic acid)

SMILES for HMDB0000413 (3-Hydroxydodecanedioic acid)

INCHI for HMDB0000413 (3-Hydroxydodecanedioic acid)

Structure for HMDB0000413 (3-Hydroxydodecanedioic acid)

3D Structure for HMDB0000413 (3-Hydroxydodecanedioic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra