MiMeDB: Showing metabocard for (R)-3-Hydroxydecanoic acid (MMDBc0047810)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:43:45 UTC

Update Date

2022-09-01 01:59:27 UTC

Metabolite ID

MMDBc0047810

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>
MMDBc0047810

> <DATABASE_NAME>
MIME

> <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

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

Molecular Formula

C₁₀H₂₀O₃

Average Mass

188.264

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-007c-9200000000-f9795d95896f66d90766	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-010c-9041000000-b9b51f3624f22e4b6c9d	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00dr-0900000000-1d9eae6ad3d5e431996b	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0fmr-3900000000-bbd0b333dda24219033a	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9200000000-7cc23eacacf566b10ff0	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-1900000000-46d09f9537cea04f6e13	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-054x-3900000000-76f4dd284af0c499a0a8	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6u-9400000000-84da3410c532bb2e2273	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-1900000000-2019592125745914c6e0	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a6r-9800000000-b6a04af2348e32c41166	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9000000000-8f7fd17dc3ad7497c377	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-009i-9800000000-2661614f9f11754f0d3a	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4l-9000000000-b7cbaa25fb90f53def32	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9000000000-6609ad3e1fed5bc9c4ca	2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191709	Fatty acid synthase	Enzyme	P49327	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019691	3-Oxodecanoic acid	(R)-3-Hydroxydecanoic acid	Not Available		PathBank	31602464
MMDBr0019692	(R)-3-Hydroxydecanoic acid	(E)-2-decenoicacid	Not Available		PathBank	31602464
MMDBr0035713	CL(10:0/10:0(3-OH)/10:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available	Deacylation	RHEA	34755880
MMDBr0028331	CL(12:0(3-OH)/10:0(3-OH)/12:0(3-OH)/10:0(3-OH))	2-MLCL(12:0(3-OH)/10:0(3-OH)/12:0(3-OH)/0:0)	Cardiolipin-specific deacylase 1, mitochondrial	Deacylation	RHEA	34755880
MMDBr0035714	CL(12:0/10:0(3-OH)/12:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available	Deacylation	RHEA	34755880
MMDBr0035715	CL(15:0/10:0(3-OH)/15:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available	Deacylation	RHEA	34755880
MMDBr0033653	CL(15:0cyclo/10:0(3-OH)/15:0cyclo/10:0(3-OH))	2-MLCL(15:0cyclo/10:0(3-OH)/15:0cyclo/0:0)	Cardiolipin-specific deacylase 1, mitochondrial	Deacylation	RHEA	34755880
MMDBr0035716	CL(16:0/10:0(3-OH)/16:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available	Deacylation	RHEA	34755880
MMDBr0035210	CL(17:0cycw7c/10:0(3-OH)/10:0/10:0)	2-MLCL(17:0cycw7c/0:0/10:0/10:0)	Cardiolipin-specific deacylase 1, mitochondrial	Deacylation	RHEA	34755880
MMDBr0035211	CL(17:0cycw7c/10:0(3-OH)/14:0/14:0)	2-MLCL(17:0cycw7c/0:0/14:0/14:0)	Cardiolipin-specific deacylase 1, mitochondrial	Deacylation	RHEA	34755880
MMDBr0035212	CL(17:0cycw7c/10:0(3-OH)/17:0cycw7c/10:0(3-OH))	2-MLCL(17:0cycw7c/10:0(3-OH)/17:0cycw7c/0:0)	Cardiolipin-specific deacylase 1, mitochondrial	Deacylation	RHEA	34755880
MMDBr0035436	CL(19:0cycv8c/10:0(3-OH)/10:0/10:0)	2-MLCL(19:0cycv8c/10:0(3-OH)/10:0/0:0)	Cardiolipin-specific deacylase 1, mitochondrial	Deacylation	RHEA	34755880
MMDBr0035437	CL(19:0cycv8c/10:0(3-OH)/19:0cycv8c/10:0(3-OH))	2-MLCL(19:0cycv8c/10:0(3-OH)/19:0cycv8c/0:0)	Cardiolipin-specific deacylase 1, mitochondrial	Deacylation	RHEA	34755880
MMDBr0035717	CL(19:iso/10:0(3-OH)/10:0/10:0)	(R)-3-Hydroxydecanoic acid	Not Available	Deacylation	RHEA	34755880
MMDBr0035520	CL(19:iso/10:0(3-OH)/19:iso/10:0(3-OH))	2-MLCL(19:iso/0:0/19:iso/10:0(3-OH))	Cardiolipin-specific deacylase 1, mitochondrial	Deacylation	RHEA	34755880
MMDBr0035718	CL(16:1(9Z)/10:0(3-OH)/16:1(9Z)/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available	Deacylation	RHEA	34755880
MMDBr0035719	CL(18:1(9Z)/10:0(3-OH)/18:1(9Z)/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available	Deacylation	RHEA	34755880
MMDBr0037474	PG(10:0(3-OH)/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037487	PG(10:0(3-OH)/19:iso)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037488	PG(10:0(3-OH)/10:0)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037520	PG(10:0(3-OH)/12:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037534	PG(10:0(3-OH)/12:0)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037563	PG(10:0(3-OH)/14:0(3-OH))	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037577	PG(10:0(3-OH)/14:0)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037656	PG(10:0(3-OH)/15:0)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037696	PG(10:0(3-OH)/15:0cyclo)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037773	PG(10:0(3-OH)/16:0)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037848	PG(10:0(3-OH)/16:1(9Z))	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037900	PG(10:0(3-OH)/17:0cycw7c)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0037979	PG(10:0(3-OH)/18:1(9Z))	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0038028	PG(10:0(3-OH)/19:0cycv8c)	(R)-3-Hydroxydecanoic acid	Not Available		RHEA	34755880
MMDBr0038383	PE(10:0(3-OH)/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038396	PE(10:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038401	PE(12:0(3-OH)/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038414	PE(12:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038419	PE(14:0(3-OH)/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038432	PE(14:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038436	PE(15:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038440	PE(15:0cyclo/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038444	PE(16:0/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038448	PE(16:1(9Z)/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038452	PE(17:0cycw7c/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038456	PE(18:1(9Z)/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038460	PE(19:0cycv8c/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0038465	PE(19:iso/10:0(3-OH))	(R)-3-Hydroxydecanoic acid	Lipid droplet phospholipase 1	Hydrolysis	RHEA	34755880
MMDBr0039051	(R)-3-Hydroxydecanoic acid	(S)-Hydroxydecanoyl-CoA	Medium/long-chain-fatty-acid--CoA/3-oxocholest-4-en-26-oate--CoA ligase (FACL) (EC 6.2.1.2) (EC 6.2.1.3) (EC 6.2.1.42) (Acyl-CoA synthetase) (FACL19) (Steroid-CoA ligase) (Steroid-coenzyme A ligase)	Hydrolysis; Ligation	RHEA	34755880
MMDBr0039584	DG(10:0(3-OH)/12:0(3-OH)/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039585	DG(10:0(3-OH)/12:0/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039586	DG(10:0(3-OH)/15:0cyclo/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039587	DG(10:0(3-OH)/16:0/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039588	DG(10:0(3-OH)/16:1(9Z)/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039589	DG(10:0(3-OH)/17:0cycw7c/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039590	DG(10:0(3-OH)/19:0cycv8c/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039591	DG(10:0(3-OH)/19:iso/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039592	DG(15:0cyclo/10:0(3-OH)/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039593	DG(17:0cycw7c/10:0(3-OH)/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039594	DG(19:0cycv8c/10:0(3-OH)/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880
MMDBr0039595	DG(19:iso/10:0(3-OH)/0:0)	(R)-3-Hydroxydecanoic acid	Carboxylesterase Culp1	Hydrolysis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0010725

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

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for (R)-3-Hydroxydecanoic acid (MMDBc0047810)

MOL for #<Metabolite:0x00007fa4d35f9130>

3D MOL for #<Metabolite:0x00007fa4d35f9130>

3D SDF for #<Metabolite:0x00007fa4d35f9130>

3D-SDF for #<Metabolite:0x00007fa4d35f9130>

PDB for #<Metabolite:0x00007fa4d35f9130>

3D PDB for #<Metabolite:0x00007fa4d35f9130>

SMILES for #<Metabolite:0x00007fa4d35f9130>

INCHI for #<Metabolite:0x00007fa4d35f9130>

Structure for #<Metabolite:0x00007fa4d35f9130>

3D Structure for #<Metabolite:0x00007fa4d35f9130>