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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2014-04-11 22:17:01 UTC

Update Date

2021-09-14 14:57:39 UTC

HMDB ID

HMDB0061655

Secondary Accession Numbers

HMDB61655

Metabolite Identification

Common Name

3-hydroxytridecanoic acid

Description

3-hydroxytridecanoic acid belongs to the class of organic compounds known as long-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 13 and 21 carbon atoms. 3-hydroxytridecanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

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

HMDB0061655
     RDKit          3D
3-hydroxytridecanoic acid
 42 41  0  0  0  0  0  0  0  0999 V2000
   -5.4836    1.3034   -0.9015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7506   -0.0341   -0.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7591   -0.4843    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3640   -0.7186    0.3075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6119    0.4298   -0.2486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1730    0.0598   -0.5889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3875   -0.4114    0.5949 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0386   -0.7772    0.2088 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7912    0.3885   -0.3762 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1867    0.0354   -0.7730 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0506   -0.4469    0.3616 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1792    0.5042    1.3616 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3773   -0.9740   -0.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2183   -0.0075   -0.8164 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3284   -0.4458   -1.2709 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9504    1.3118   -1.0491 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1852    1.1843   -1.9719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4621    1.8994   -0.9948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8049    1.9070   -0.2933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7431    0.0621    0.2550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9612   -0.8119   -1.0676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7596    0.2290    1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1156   -1.4487    1.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2572   -1.6326   -0.3367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8155   -1.0254    1.2587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0277    0.7521   -1.2476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5946    1.3077    0.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7171    1.0304   -0.9315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0951   -0.6344   -1.4336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8178   -1.2924    1.0979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2952    0.3841    1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5716   -1.1147    1.1404 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0182   -1.5703   -0.5456 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8722    1.1868    0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2633    0.8465   -1.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1856   -0.7156   -1.6147 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6947    0.9448   -1.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5195   -1.3168    0.8422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1779    1.3993    0.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9009   -1.4734    0.7493 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1714   -1.8138   -0.8305 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6857    1.9831   -1.1511 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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  6 29  1  0
  7 30  1  0
  7 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
  9 35  1  0
 10 36  1  0
 10 37  1  0
 11 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 16 42  1  0
M  END


  Mrv0541 04111415172D          

 16 15  0  0  0  0            999 V2000
    5.4730    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7586    3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4730    4.8099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9020    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9020    4.8099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6164    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3309    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0454    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7599    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1888    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9033    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6177    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3322    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0467    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  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
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0061655

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCC(O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H26O3/c1-2-3-4-5-6-7-8-9-10-12(14)11-13(15)16/h12,14H,2-11H2,1H3,(H,15,16)

> <INCHI_KEY>
CWSNHZHHWHLJIM-UHFFFAOYSA-N

> <FORMULA>
C13H26O3

> <MOLECULAR_WEIGHT>
230.3437

> <EXACT_MASS>
230.188194698

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
28.718762335362555

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxytridecanoic acid

> <ALOGPS_LOGP>
4.15

> <JCHEM_LOGP>
3.692065715666666

> <ALOGPS_LOGS>
-3.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.288498288670866

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.671850167040888

> <JCHEM_PKA_STRONGEST_BASIC>
-2.798587426318786

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
64.7961

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.93e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxytridecanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0061655
     RDKit          3D
3-hydroxytridecanoic acid
 42 41  0  0  0  0  0  0  0  0999 V2000
   -5.4836    1.3034   -0.9015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7506   -0.0341   -0.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7591   -0.4843    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3640   -0.7186    0.3075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6119    0.4298   -0.2486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1730    0.0598   -0.5889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3875   -0.4114    0.5949 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0386   -0.7772    0.2088 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7912    0.3885   -0.3762 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1867    0.0354   -0.7730 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0506   -0.4469    0.3616 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1792    0.5042    1.3616 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3773   -0.9740   -0.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2183   -0.0075   -0.8164 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3284   -0.4458   -1.2709 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9504    1.3118   -1.0491 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1852    1.1843   -1.9719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4621    1.8994   -0.9948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8049    1.9070   -0.2933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7431    0.0621    0.2550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9612   -0.8119   -1.0676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7596    0.2290    1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1156   -1.4487    1.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2572   -1.6326   -0.3367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8155   -1.0254    1.2587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0277    0.7521   -1.2476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5946    1.3077    0.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7171    1.0304   -0.9315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0951   -0.6344   -1.4336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8178   -1.2924    1.0979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2952    0.3841    1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5716   -1.1147    1.1404 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0182   -1.5703   -0.5456 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8722    1.1868    0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2633    0.8465   -1.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1856   -0.7156   -1.6147 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6947    0.9448   -1.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5195   -1.3168    0.8422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1779    1.3993    0.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9009   -1.4734    0.7493 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1714   -1.8138   -0.8305 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6857    1.9831   -1.1511 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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  6 29  1  0
  7 30  1  0
  7 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
  9 35  1  0
 10 36  1  0
 10 37  1  0
 11 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 16 42  1  0
M  END

HEADER    PROTEIN                                 11-APR-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-APR-14         0                                  
HETATM    1  C   UNK     0      10.216   7.438   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       8.883   6.668   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      10.216   8.978   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      11.550   6.668   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.884   7.438   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      12.884   8.978   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      14.217   6.668   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.551   7.438   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      16.885   6.668   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.218   7.438   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.552   6.668   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.886   7.438   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      22.219   6.668   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      23.553   7.438   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      24.887   6.668   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      26.221   7.438   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

COMPND    HMDB0061655
HETATM    1  C1  UNL     1      -5.484   1.303  -0.902  1.00  0.00           C  
HETATM    2  C2  UNL     1      -5.751  -0.034  -0.288  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.759  -0.484   0.708  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.364  -0.719   0.308  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.612   0.430  -0.249  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.173   0.060  -0.589  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.388  -0.411   0.595  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.039  -0.777   0.209  1.00  0.00           C  
HETATM    9  C9  UNL     1       1.791   0.388  -0.376  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.187   0.035  -0.773  1.00  0.00           C  
HETATM   11  C11 UNL     1       4.051  -0.447   0.362  1.00  0.00           C  
HETATM   12  O1  UNL     1       4.179   0.504   1.362  1.00  0.00           O  
HETATM   13  C12 UNL     1       5.377  -0.974  -0.105  1.00  0.00           C  
HETATM   14  C13 UNL     1       6.218  -0.007  -0.816  1.00  0.00           C  
HETATM   15  O2  UNL     1       7.328  -0.446  -1.271  1.00  0.00           O  
HETATM   16  O3  UNL     1       5.950   1.312  -1.049  1.00  0.00           O  
HETATM   17  H1  UNL     1      -5.185   1.184  -1.972  1.00  0.00           H  
HETATM   18  H2  UNL     1      -6.462   1.899  -0.995  1.00  0.00           H  
HETATM   19  H3  UNL     1      -4.805   1.907  -0.293  1.00  0.00           H  
HETATM   20  H4  UNL     1      -6.743   0.062   0.255  1.00  0.00           H  
HETATM   21  H5  UNL     1      -5.961  -0.812  -1.068  1.00  0.00           H  
HETATM   22  H6  UNL     1      -4.760   0.229   1.588  1.00  0.00           H  
HETATM   23  H7  UNL     1      -5.116  -1.449   1.206  1.00  0.00           H  
HETATM   24  H8  UNL     1      -3.257  -1.633  -0.337  1.00  0.00           H  
HETATM   25  H9  UNL     1      -2.815  -1.025   1.259  1.00  0.00           H  
HETATM   26  H10 UNL     1      -3.028   0.752  -1.248  1.00  0.00           H  
HETATM   27  H11 UNL     1      -2.595   1.308   0.386  1.00  0.00           H  
HETATM   28  H12 UNL     1      -0.717   1.030  -0.931  1.00  0.00           H  
HETATM   29  H13 UNL     1      -1.095  -0.634  -1.434  1.00  0.00           H  
HETATM   30  H14 UNL     1      -0.818  -1.292   1.098  1.00  0.00           H  
HETATM   31  H15 UNL     1      -0.295   0.384   1.376  1.00  0.00           H  
HETATM   32  H16 UNL     1       1.572  -1.115   1.140  1.00  0.00           H  
HETATM   33  H17 UNL     1       1.018  -1.570  -0.546  1.00  0.00           H  
HETATM   34  H18 UNL     1       1.872   1.187   0.414  1.00  0.00           H  
HETATM   35  H19 UNL     1       1.263   0.847  -1.235  1.00  0.00           H  
HETATM   36  H20 UNL     1       3.186  -0.716  -1.615  1.00  0.00           H  
HETATM   37  H21 UNL     1       3.695   0.945  -1.206  1.00  0.00           H  
HETATM   38  H22 UNL     1       3.519  -1.317   0.842  1.00  0.00           H  
HETATM   39  H23 UNL     1       4.178   1.399   0.905  1.00  0.00           H  
HETATM   40  H24 UNL     1       5.901  -1.473   0.749  1.00  0.00           H  
HETATM   41  H25 UNL     1       5.171  -1.814  -0.830  1.00  0.00           H  
HETATM   42  H26 UNL     1       6.686   1.983  -1.151  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3   20   21
CONECT    3    4   22   23
CONECT    4    5   24   25
CONECT    5    6   26   27
CONECT    6    7   28   29
CONECT    7    8   30   31
CONECT    8    9   32   33
CONECT    9   10   34   35
CONECT   10   11   36   37
CONECT   11   12   13   38
CONECT   12   39
CONECT   13   14   40   41
CONECT   14   15   15   16
CONECT   16   42
END

HMDB0061655
     RDKit          3D
3-hydroxytridecanoic acid
 42 41  0  0  0  0  0  0  0  0999 V2000
   -5.4836    1.3034   -0.9015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7506   -0.0341   -0.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7591   -0.4843    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3640   -0.7186    0.3075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6119    0.4298   -0.2486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1730    0.0598   -0.5889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3875   -0.4114    0.5949 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0386   -0.7772    0.2088 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7912    0.3885   -0.3762 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1867    0.0354   -0.7730 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0506   -0.4469    0.3616 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1792    0.5042    1.3616 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3773   -0.9740   -0.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2183   -0.0075   -0.8164 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3284   -0.4458   -1.2709 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9504    1.3118   -1.0491 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1852    1.1843   -1.9719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4621    1.8994   -0.9948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8049    1.9070   -0.2933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7431    0.0621    0.2550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9612   -0.8119   -1.0676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7596    0.2290    1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1156   -1.4487    1.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2572   -1.6326   -0.3367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8155   -1.0254    1.2587 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0277    0.7521   -1.2476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5946    1.3077    0.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7171    1.0304   -0.9315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0951   -0.6344   -1.4336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8178   -1.2924    1.0979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2952    0.3841    1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5716   -1.1147    1.1404 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0182   -1.5703   -0.5456 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8722    1.1868    0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2633    0.8465   -1.2352 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1856   -0.7156   -1.6147 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6947    0.9448   -1.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5195   -1.3168    0.8422 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1779    1.3993    0.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9009   -1.4734    0.7493 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1714   -1.8138   -0.8305 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6857    1.9831   -1.1511 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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  6 29  1  0
  7 30  1  0
  7 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
  9 35  1  0
 10 36  1  0
 10 37  1  0
 11 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 16 42  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Hydroxytridecanoate	Generator
3-Hydroxy-tridecanoate	Generator

Chemical Formula

C₁₃H₂₆O₃

Average Molecular Weight

230.3437

Monoisotopic Molecular Weight

230.188194698

IUPAC Name

3-hydroxytridecanoic acid

Traditional Name

3-hydroxytridecanoic acid

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCC(O)CC(O)=O

InChI Identifier

InChI=1S/C13H26O3/c1-2-3-4-5-6-7-8-9-10-12(14)11-13(15)16/h12,14H,2-11H2,1H3,(H,15,16)

InChI Key

CWSNHZHHWHLJIM-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as long-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 13 and 21 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Long-chain fatty acids

Alternative Parents

Substituents

Long-chain fatty acid
Beta-hydroxy acid
Branched fatty acid
Methyl-branched fatty acid
Hydroxy fatty acid
Hydroxy acid
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organooxygen compound
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Hydroxy fatty acids (LMFA01050172 )

Ontology

Not Available

Exogenous (HMDB: HMDB0061655)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

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	0.079 g/L	ALOGPS
logP	4.15	ALOGPS
logP	3.69	ChemAxon
logS	-3.5	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	11	ChemAxon
Refractivity	64.8 m³·mol⁻¹	ChemAxon
Polarizability	28.72 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]+	158.137	31661259
DarkChem	[M-H]-	155.995	31661259
DeepCCS	[M+H]+	157.688	30932474
DeepCCS	[M-H]-	153.663	30932474
DeepCCS	[M-2H]-	190.754	30932474
DeepCCS	[M+Na]+	166.611	30932474
AllCCS	[M+H]+	161.2	32859911
AllCCS	[M+H-H2O]+	157.8	32859911
AllCCS	[M+NH4]+	164.4	32859911
AllCCS	[M+Na]+	165.3	32859911
AllCCS	[M-H]-	160.5	32859911
AllCCS	[M+Na-2H]-	161.5	32859911
AllCCS	[M+HCOO]-	162.8	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.	8.41 minutes	32390414
Predicted by Siyang on May 30, 2022	14.3125 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.77 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2323.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	341.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	168.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	187.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	404.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	640.2 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	606.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	103.6 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1290.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	460.8 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	1449.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	436.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	374.4 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	278.2 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	44.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-hydroxytridecanoic acid	CCCCCCCCCCC(O)CC(O)=O	3069.8	Standard polar	33892256
3-hydroxytridecanoic acid	CCCCCCCCCCC(O)CC(O)=O	1738.3	Standard non polar	33892256
3-hydroxytridecanoic acid	CCCCCCCCCCC(O)CC(O)=O	1852.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-hydroxytridecanoic acid,1TMS,isomer #1	CCCCCCCCCCC(CC(=O)O)O[Si](C)(C)C	1889.4	Semi standard non polar	33892256
3-hydroxytridecanoic acid,1TMS,isomer #2	CCCCCCCCCCC(O)CC(=O)O[Si](C)(C)C	1884.7	Semi standard non polar	33892256
3-hydroxytridecanoic acid,2TMS,isomer #1	CCCCCCCCCCC(CC(=O)O[Si](C)(C)C)O[Si](C)(C)C	1938.7	Semi standard non polar	33892256
3-hydroxytridecanoic acid,1TBDMS,isomer #1	CCCCCCCCCCC(CC(=O)O)O[Si](C)(C)C(C)(C)C	2123.5	Semi standard non polar	33892256
3-hydroxytridecanoic acid,1TBDMS,isomer #2	CCCCCCCCCCC(O)CC(=O)O[Si](C)(C)C(C)(C)C	2126.8	Semi standard non polar	33892256
3-hydroxytridecanoic acid,2TBDMS,isomer #1	CCCCCCCCCCC(CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2385.5	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-hydroxytridecanoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-000f-9500000000-25366595d2ff7deca1e6	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-hydroxytridecanoic acid GC-MS (2 TMS) - 70eV, Positive	splash10-05bo-9132000000-3a025be71d416ab68d03	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-hydroxytridecanoic 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 - 3-hydroxytridecanoic acid 10V, Positive-QTOF	splash10-03di-0490000000-dd77c808b28d6c70c3da	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 20V, Positive-QTOF	splash10-03dj-4940000000-e961beef0102305256ae	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 40V, Positive-QTOF	splash10-052f-9300000000-d8d27d76029fe8f48404	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 10V, Negative-QTOF	splash10-004i-0390000000-2d728f4c44930eafdfea	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 20V, Negative-QTOF	splash10-092i-3970000000-45ffbc64b3d881340413	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 40V, Negative-QTOF	splash10-05mo-9600000000-d3d36f34ec965d669ede	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 10V, Negative-QTOF	splash10-056r-7090000000-03563bd33fba9aa6209e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 20V, Negative-QTOF	splash10-0a4i-9000000000-9c4d42e79dd9a1e6e330	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 40V, Negative-QTOF	splash10-0006-9000000000-24256337cd6db4163a77	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 10V, Positive-QTOF	splash10-001i-9470000000-51f295e6f06d23760364	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 20V, Positive-QTOF	splash10-0avr-9000000000-8d3fc13af9b24e00eda7	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxytridecanoic acid 40V, Positive-QTOF	splash10-0a4l-9000000000-85981ddded053d2fbab7	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5312749

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

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.
The AOCS Lipid Library [Link]

Showing metabocard for 3-hydroxytridecanoic acid (HMDB0061655)

MOL for HMDB0061655 (3-hydroxytridecanoic acid)

3D MOL for HMDB0061655 (3-hydroxytridecanoic acid)

3D SDF for HMDB0061655 (3-hydroxytridecanoic acid)

3D-SDF for HMDB0061655 (3-hydroxytridecanoic acid)

PDB for HMDB0061655 (3-hydroxytridecanoic acid)

3D PDB for HMDB0061655 (3-hydroxytridecanoic acid)

SMILES for HMDB0061655 (3-hydroxytridecanoic acid)

INCHI for HMDB0061655 (3-hydroxytridecanoic acid)

Structure for HMDB0061655 (3-hydroxytridecanoic acid)

3D Structure for HMDB0061655 (3-hydroxytridecanoic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra