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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2008-10-15 12:12:16 UTC

Update Date

2022-09-22 18:34:19 UTC

HMDB ID

HMDB0010725

Secondary Accession Numbers

HMDB10725

Metabolite Identification

Common Name

(R)-3-Hydroxydecanoic acid

Description

(R)-3-Hydroxydecanoic acid, also known as 3-HDA or myrmicacin, 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 (R)-3-Hydroxydecanoic acid exists in all eukaryotes, ranging from yeast to plants to humans. In humans, (R)-3-hydroxydecanoic acid is involved in the fatty acid biosynthesis pathway (R)-3-Hydroxydecanoic 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 (R)-3-hydroxydecanoic acid a potential biomarker for the consumption of these foods (R)-3-Hydroxydecanoic 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 very few articles have been published on (R)-3-Hydroxydecanoic acid.

Structure

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

HMDB0010725
     RDKit          3D
(R)-3-Hydroxydecanoic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    4.9488    0.0134    0.1163 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1045   -1.0176   -0.5489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6935   -1.1029   -0.0756 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9066    0.1677   -0.2538 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4658   -0.0083    0.2427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2239    1.2803    0.0270 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6703    1.3446    0.4138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5671    0.4104   -0.3324 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2323   -0.9333   -0.1849 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9588    0.5434    0.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9183   -0.3491   -0.3699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7455    0.1806   -1.1419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8488   -1.7103   -0.1293 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5092   -0.4088    0.9986 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7485    0.3524   -0.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4294    0.9185    0.4471 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741   -2.0259   -0.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1435   -0.8411   -1.6663 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1856   -1.9188   -0.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7328   -1.3626    1.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106    0.4869   -1.3259 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4125    0.9719    0.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5539   -0.2868    1.3199 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0752   -0.8522   -0.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1106    1.5782   -1.0346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3144    2.0502    0.6142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8316    1.2339    1.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0096    2.3861    0.1812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7094    0.7191   -1.3843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1492   -1.3446   -1.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8756    0.2696    1.3910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2691    1.6065    0.2830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5888   -2.3514   -0.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
  8 29  1  6
  9 30  1  0
 10 31  1  0
 10 32  1  0
 13 33  1  0
M  END


  Mrv0541 02241201182D          

 14 13  0  0  1  0            999 V2000
   10.4123   -7.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1267   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8413   -7.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5557   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2702   -7.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9847   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6992   -7.0554    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.4136   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1281   -7.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8426   -7.4679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1281   -6.2304    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1118   -6.4122    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6978   -7.4679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1578   -6.4462    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  2  0  0  0  0
 11  9  1  0  0  0  0
  7 12  1  1  0  0  0
  1 13  1  0  0  0  0
  7 14  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0010725

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H20O3/c1-2-3-4-5-6-7-9(11)8-10(12)13/h9,11H,2-8H2,1H3,(H,12,13)/t9-/m1/s1

> <INCHI_KEY>
FYSSBMZUBSBFJL-SECBINFHSA-N

> <FORMULA>
C10H20O3

> <MOLECULAR_WEIGHT>
188.264

> <EXACT_MASS>
188.141244506

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
22.346980006857343

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.60

> <JCHEM_LOGP>
2.358359720666666

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.288498288675335

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.671850167040888

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7985874263168293

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
50.9931

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.74e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0010725
     RDKit          3D
(R)-3-Hydroxydecanoic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    4.9488    0.0134    0.1163 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1045   -1.0176   -0.5489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6935   -1.1029   -0.0756 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9066    0.1677   -0.2538 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4658   -0.0083    0.2427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2239    1.2803    0.0270 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6703    1.3446    0.4138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5671    0.4104   -0.3324 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2323   -0.9333   -0.1849 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9588    0.5434    0.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9183   -0.3491   -0.3699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7455    0.1806   -1.1419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8488   -1.7103   -0.1293 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5092   -0.4088    0.9986 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7485    0.3524   -0.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4294    0.9185    0.4471 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741   -2.0259   -0.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1435   -0.8411   -1.6663 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1856   -1.9188   -0.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7328   -1.3626    1.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106    0.4869   -1.3259 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4125    0.9719    0.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5539   -0.2868    1.3199 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0752   -0.8522   -0.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1106    1.5782   -1.0346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3144    2.0502    0.6142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8316    1.2339    1.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0096    2.3861    0.1812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7094    0.7191   -1.3843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1492   -1.3446   -1.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8756    0.2696    1.3910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2691    1.6065    0.2830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5888   -2.3514   -0.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
  8 29  1  6
  9 30  1  0
 10 31  1  0
 10 32  1  0
 13 33  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      19.436 -13.170   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.770 -13.940   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      22.104 -13.170   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      23.437 -13.940   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      24.771 -13.170   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.105 -13.940   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      27.439 -13.170   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      28.772 -13.940   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.106 -13.170   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      31.440 -13.940   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      30.106 -11.630   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      26.342 -11.969   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      18.103 -13.940   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0      28.295 -12.033   0.000  0.00  0.00           H+0
CONECT    1    2   13                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   12   14                                             
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7                                                            
CONECT   13    1                                                            
CONECT   14    7                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

COMPND    HMDB0010725
HETATM    1  C1  UNL     1       4.949   0.013   0.116  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.105  -1.018  -0.549  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.694  -1.103  -0.076  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.907   0.168  -0.254  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.466  -0.008   0.243  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.224   1.280   0.027  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.670   1.345   0.414  1.00  0.00           C  
HETATM    8  C8  UNL     1      -2.567   0.410  -0.332  1.00  0.00           C  
HETATM    9  O1  UNL     1      -2.232  -0.933  -0.185  1.00  0.00           O  
HETATM   10  C9  UNL     1      -3.959   0.543   0.322  1.00  0.00           C  
HETATM   11  C10 UNL     1      -4.918  -0.349  -0.370  1.00  0.00           C  
HETATM   12  O2  UNL     1      -5.745   0.181  -1.142  1.00  0.00           O  
HETATM   13  O3  UNL     1      -4.849  -1.710  -0.129  1.00  0.00           O  
HETATM   14  H1  UNL     1       5.509  -0.409   0.999  1.00  0.00           H  
HETATM   15  H2  UNL     1       5.748   0.352  -0.610  1.00  0.00           H  
HETATM   16  H3  UNL     1       4.429   0.918   0.447  1.00  0.00           H  
HETATM   17  H4  UNL     1       4.574  -2.026  -0.402  1.00  0.00           H  
HETATM   18  H5  UNL     1       4.143  -0.841  -1.666  1.00  0.00           H  
HETATM   19  H6  UNL     1       2.186  -1.919  -0.615  1.00  0.00           H  
HETATM   20  H7  UNL     1       2.733  -1.363   1.014  1.00  0.00           H  
HETATM   21  H8  UNL     1       1.911   0.487  -1.326  1.00  0.00           H  
HETATM   22  H9  UNL     1       2.412   0.972   0.315  1.00  0.00           H  
HETATM   23  H10 UNL     1       0.554  -0.287   1.320  1.00  0.00           H  
HETATM   24  H11 UNL     1       0.075  -0.852  -0.344  1.00  0.00           H  
HETATM   25  H12 UNL     1      -0.111   1.578  -1.035  1.00  0.00           H  
HETATM   26  H13 UNL     1       0.314   2.050   0.614  1.00  0.00           H  
HETATM   27  H14 UNL     1      -1.832   1.234   1.502  1.00  0.00           H  
HETATM   28  H15 UNL     1      -2.010   2.386   0.181  1.00  0.00           H  
HETATM   29  H16 UNL     1      -2.709   0.719  -1.384  1.00  0.00           H  
HETATM   30  H17 UNL     1      -2.149  -1.345  -1.079  1.00  0.00           H  
HETATM   31  H18 UNL     1      -3.876   0.270   1.391  1.00  0.00           H  
HETATM   32  H19 UNL     1      -4.269   1.607   0.283  1.00  0.00           H  
HETATM   33  H20 UNL     1      -5.589  -2.351  -0.388  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3   17   18
CONECT    3    4   19   20
CONECT    4    5   21   22
CONECT    5    6   23   24
CONECT    6    7   25   26
CONECT    7    8   27   28
CONECT    8    9   10   29
CONECT    9   30
CONECT   10   11   31   32
CONECT   11   12   12   13
CONECT   13   33
END

HMDB0010725
     RDKit          3D
(R)-3-Hydroxydecanoic acid
 33 32  0  0  0  0  0  0  0  0999 V2000
    4.9488    0.0134    0.1163 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1045   -1.0176   -0.5489 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6935   -1.1029   -0.0756 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9066    0.1677   -0.2538 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4658   -0.0083    0.2427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2239    1.2803    0.0270 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6703    1.3446    0.4138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5671    0.4104   -0.3324 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2323   -0.9333   -0.1849 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9588    0.5434    0.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9183   -0.3491   -0.3699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7455    0.1806   -1.1419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8488   -1.7103   -0.1293 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5092   -0.4088    0.9986 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7485    0.3524   -0.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4294    0.9185    0.4471 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741   -2.0259   -0.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1435   -0.8411   -1.6663 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1856   -1.9188   -0.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7328   -1.3626    1.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106    0.4869   -1.3259 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4125    0.9719    0.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5539   -0.2868    1.3199 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0752   -0.8522   -0.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1106    1.5782   -1.0346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3144    2.0502    0.6142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8316    1.2339    1.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0096    2.3861    0.1812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7094    0.7191   -1.3843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1492   -1.3446   -1.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8756    0.2696    1.3910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2691    1.6065    0.2830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5888   -2.3514   -0.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
  8 29  1  6
  9 30  1  0
 10 31  1  0
 10 32  1  0
 13 33  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(R)-3-Hydroxydecanoate	Generator
3-HDA	HMDB
3-Hydroxydecanoic acid	HMDB
beta-Hydroxydecanoic acid	HMDB
Myrmicacin, (+-)-isomer	HMDB
Myrmicacin monosodium (+-)-isomer	HMDB
3-Hydroxy-decanoic acid	HMDB
Myrmicacin, (R)-isomer	HMDB
Myrmicacin	HMDB

Chemical Formula

C₁₀H₂₀O₃

Average Molecular Weight

188.264

Monoisotopic Molecular Weight

188.141244506

IUPAC Name

(3R)-3-hydroxydecanoic acid

Traditional Name

(R)-3-hydroxydecanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C10H20O3/c1-2-3-4-5-6-7-9(11)8-10(12)13/h9,11H,2-8H2,1H3,(H,12,13)/t9-/m1/s1

InChI Key

FYSSBMZUBSBFJL-SECBINFHSA-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
Fatty acyl
Fatty acid
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxide
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Hydroxy fatty acids (LMFA01050245 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0010725)
Cell membrane (HMDB: HMDB0010725)

Source

Endogenous

Endogenous (HMDB: HMDB0010725)

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

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Fatty Acid Biosynthesis (PathBank: SMP0002360)
Fatty Acid Biosynthesis (PathBank: SMP0087409)
Fatty Acid Biosynthesis (HMDB: HMDB0010725)

Role

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	1.74 g/L	ALOGPS
logP	2.6	ALOGPS
logP	2.36	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	4.67	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	50.99 m³·mol⁻¹	ChemAxon
Polarizability	22.35 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]+	147.41	31661259
DarkChem	[M-H]-	144.418	31661259
DeepCCS	[M+H]+	144.635	30932474
DeepCCS	[M-H]-	141.773	30932474
DeepCCS	[M-2H]-	178.645	30932474
DeepCCS	[M+Na]+	154.182	30932474
AllCCS	[M+H]+	147.7	32859911
AllCCS	[M+H-H2O]+	143.9	32859911
AllCCS	[M+NH4]+	151.2	32859911
AllCCS	[M+Na]+	152.2	32859911
AllCCS	[M-H]-	146.7	32859911
AllCCS	[M+Na-2H]-	148.1	32859911
AllCCS	[M+HCOO]-	149.7	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	6.06 minutes	32390414
Predicted by Siyang on May 30, 2022	11.6304 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.06 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	48.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1856.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	304.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	142.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	183.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	274.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	497.0 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	493.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	99.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	998.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	389.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1273.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	321.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	328.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	396.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	207.6 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	87.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(R)-3-Hydroxydecanoic acid	[H][C@@](O)(CCCCCCC)CC(O)=O	2632.9	Standard polar	33892256
(R)-3-Hydroxydecanoic acid	[H][C@@](O)(CCCCCCC)CC(O)=O	1487.9	Standard non polar	33892256
(R)-3-Hydroxydecanoic acid	[H][C@@](O)(CCCCCCC)CC(O)=O	1569.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(R)-3-Hydroxydecanoic acid,1TMS,isomer #1	CCCCCCC[C@H](CC(=O)O)O[Si](C)(C)C	1582.5	Semi standard non polar	33892256
(R)-3-Hydroxydecanoic acid,1TMS,isomer #2	CCCCCCC[C@@H](O)CC(=O)O[Si](C)(C)C	1570.1	Semi standard non polar	33892256
(R)-3-Hydroxydecanoic acid,2TMS,isomer #1	CCCCCCC[C@H](CC(=O)O[Si](C)(C)C)O[Si](C)(C)C	1665.8	Semi standard non polar	33892256
(R)-3-Hydroxydecanoic acid,1TBDMS,isomer #1	CCCCCCC[C@H](CC(=O)O)O[Si](C)(C)C(C)(C)C	1804.3	Semi standard non polar	33892256
(R)-3-Hydroxydecanoic acid,1TBDMS,isomer #2	CCCCCCC[C@@H](O)CC(=O)O[Si](C)(C)C(C)(C)C	1799.5	Semi standard non polar	33892256
(R)-3-Hydroxydecanoic acid,2TBDMS,isomer #1	CCCCCCC[C@H](CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2122.0	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 - (R)-3-Hydroxydecanoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-007c-9200000000-f9795d95896f66d90766	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (R)-3-Hydroxydecanoic acid GC-MS (2 TMS) - 70eV, Positive	splash10-010c-9041000000-b9b51f3624f22e4b6c9d	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (R)-3-Hydroxydecanoic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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 - (R)-3-Hydroxydecanoic acid 10V, Positive-QTOF	splash10-00dr-0900000000-1d9eae6ad3d5e431996b	2016-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 20V, Positive-QTOF	splash10-0fmr-3900000000-bbd0b333dda24219033a	2016-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 40V, Positive-QTOF	splash10-052f-9200000000-7cc23eacacf566b10ff0	2016-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 10V, Negative-QTOF	splash10-000i-1900000000-46d09f9537cea04f6e13	2016-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 20V, Negative-QTOF	splash10-054x-3900000000-76f4dd284af0c499a0a8	2016-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 40V, Negative-QTOF	splash10-0a6u-9400000000-84da3410c532bb2e2273	2016-09-14	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 10V, Negative-QTOF	splash10-000i-1900000000-2019592125745914c6e0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 20V, Negative-QTOF	splash10-0a6r-9800000000-b6a04af2348e32c41166	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 40V, Negative-QTOF	splash10-052f-9000000000-8f7fd17dc3ad7497c377	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 10V, Positive-QTOF	splash10-009i-9800000000-2661614f9f11754f0d3a	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 20V, Positive-QTOF	splash10-0a4l-9000000000-b7cbaa25fb90f53def32	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 40V, Positive-QTOF	splash10-0a4l-9000000000-6609ad3e1fed5bc9c4ca	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Fatty Acid Biosynthesis		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB027873

KNApSAcK ID

Not Available

Chemspider ID

4472223

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5312798

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

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Fatty acid synthase

General function:: Involved in transferase activity
Specific function:: Fatty acid synthetase catalyzes the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. This multifunctional protein has 7 catalytic activities and an acyl carrier protein.
Gene Name:: FASN
Uniprot ID:: P49327
Molecular weight:: 273424.06

Showing metabocard for (R)-3-Hydroxydecanoic acid (HMDB0010725)

MOL for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

3D MOL for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

3D SDF for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

3D-SDF for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

PDB for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

3D PDB for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

SMILES for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

INCHI for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

Structure for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

3D Structure for HMDB0010725 ((R)-3-Hydroxydecanoic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes