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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:42:45 UTC

Update Date

2022-03-07 02:56:29 UTC

HMDB ID

HMDB0040169

Secondary Accession Numbers

HMDB40169

Metabolite Identification

Common Name

xi-5-Hydroxydodecanoic acid

Description

xi-5-Hydroxydodecanoic acid belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. Based on a literature review a small amount of articles have been published on xi-5-Hydroxydodecanoic acid.

Structure

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

HMDB0040169
     RDKit          3D
xi-5-Hydroxydodecanoic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.2944    1.0513    0.5691 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2228   -0.3299   -0.0383 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8073   -0.8770    0.0483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8550    0.0133   -0.6863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4230   -0.4824   -0.6388 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9450   -0.5644    0.7679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485   -1.0500    0.9178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5152   -0.2429    0.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4178   -0.1065   -1.0997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8450   -0.9176    0.6013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0040   -0.1943   -0.0052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1361    1.2331    0.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3111    1.8171   -0.2221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2159    2.2012   -1.4145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5059    1.9378    0.4604 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3187    1.1855    0.9917 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5804    1.1492    1.4142 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1353    1.8404   -0.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5897   -0.3076   -1.0682 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8890   -0.9887    0.5734 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7629   -1.8801   -0.3980 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5948   -0.9830    1.1270 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1523    0.0074   -1.7547 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8800    1.0621   -0.3550 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3243   -1.4341   -1.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8459    0.2869   -1.2224 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1175    0.4158    1.2618 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6001   -1.3001    1.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7023   -1.0664    2.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4679   -2.1236    0.6115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4697    0.7812    0.6957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7554   -0.9364   -1.5296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9209   -1.0644    1.6857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8067   -1.9270    0.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9213   -0.2823   -1.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9246   -0.7256    0.2873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2477    1.8447    0.1707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3135    1.2212    1.5360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4087    1.7361    0.0096 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  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 11 36  1  0
 12 37  1  0
 12 38  1  0
 15 39  1  0
M  END


  Mrv0541 05061311402D          

 15 14  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
    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
    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
   11.9033    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
   11.1888    3.9849    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
   10.4743    3.5724    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
   10.4743    2.7474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.0467    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3322    2.7474    0.0000 O   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
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  7  1  0  0  0  0
 11  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  2  0  0  0  0
 15 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040169

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCC(O)CCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H24O3/c1-2-3-4-5-6-8-11(13)9-7-10-12(14)15/h11,13H,2-10H2,1H3,(H,14,15)

> <INCHI_KEY>
LXNOENXQFNYMGT-UHFFFAOYSA-N

> <FORMULA>
C12H24O3

> <MOLECULAR_WEIGHT>
216.3172

> <EXACT_MASS>
216.172544634

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
26.598489758429224

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-hydroxydodecanoic acid

> <ALOGPS_LOGP>
3.55

> <JCHEM_LOGP>
3.0915895906666666

> <ALOGPS_LOGS>
-2.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.55174111823514

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.707691911765773

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2452689921380449

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
60.34910000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.66e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxydodecanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0040169
     RDKit          3D
xi-5-Hydroxydodecanoic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.2944    1.0513    0.5691 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2228   -0.3299   -0.0383 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8073   -0.8770    0.0483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8550    0.0133   -0.6863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4230   -0.4824   -0.6388 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9450   -0.5644    0.7679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485   -1.0500    0.9178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5152   -0.2429    0.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4178   -0.1065   -1.0997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8450   -0.9176    0.6013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0040   -0.1943   -0.0052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1361    1.2331    0.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3111    1.8171   -0.2221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2159    2.2012   -1.4145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5059    1.9378    0.4604 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3187    1.1855    0.9917 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5804    1.1492    1.4142 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1353    1.8404   -0.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5897   -0.3076   -1.0682 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8890   -0.9887    0.5734 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7629   -1.8801   -0.3980 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5948   -0.9830    1.1270 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1523    0.0074   -1.7547 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8800    1.0621   -0.3550 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3243   -1.4341   -1.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8459    0.2869   -1.2224 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1175    0.4158    1.2618 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6001   -1.3001    1.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7023   -1.0664    2.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4679   -2.1236    0.6115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4697    0.7812    0.6957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7554   -0.9364   -1.5296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9209   -1.0644    1.6857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8067   -1.9270    0.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9213   -0.2823   -1.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9246   -0.7256    0.2873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2477    1.8447    0.1707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3135    1.2212    1.5360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4087    1.7361    0.0096 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  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 11 36  1  0
 12 37  1  0
 12 38  1  0
 15 39  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      10.216   7.438   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.550   6.668   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.884   7.438   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.217   6.668   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.551   7.438   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.885   6.668   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.219   6.668   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.218   7.438   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      20.886   7.438   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      23.553   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      24.887   6.668   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      19.552   5.128   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      26.221   7.438   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      24.887   5.128   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    8                                                       
CONECT    7    9   10                                                       
CONECT    8    6   11                                                       
CONECT    9    7   11                                                       
CONECT   10    7   12                                                       
CONECT   11    8    9   13                                                  
CONECT   12   10   14   15                                                  
CONECT   13   11                                                            
CONECT   14   12                                                            
CONECT   15   12                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

COMPND    HMDB0040169
HETATM    1  C1  UNL     1       5.294   1.051   0.569  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.223  -0.330  -0.038  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.807  -0.877   0.048  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.855   0.013  -0.686  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.423  -0.482  -0.639  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.945  -0.564   0.768  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.448  -1.050   0.918  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.515  -0.243   0.262  1.00  0.00           C  
HETATM    9  O1  UNL     1      -1.418  -0.106  -1.100  1.00  0.00           O  
HETATM   10  C9  UNL     1      -2.845  -0.918   0.601  1.00  0.00           C  
HETATM   11  C10 UNL     1      -4.004  -0.194  -0.005  1.00  0.00           C  
HETATM   12  C11 UNL     1      -4.136   1.233   0.452  1.00  0.00           C  
HETATM   13  C12 UNL     1      -5.311   1.817  -0.222  1.00  0.00           C  
HETATM   14  O2  UNL     1      -5.216   2.201  -1.415  1.00  0.00           O  
HETATM   15  O3  UNL     1      -6.506   1.938   0.460  1.00  0.00           O  
HETATM   16  H1  UNL     1       6.319   1.185   0.992  1.00  0.00           H  
HETATM   17  H2  UNL     1       4.580   1.149   1.414  1.00  0.00           H  
HETATM   18  H3  UNL     1       5.135   1.840  -0.209  1.00  0.00           H  
HETATM   19  H4  UNL     1       5.590  -0.308  -1.068  1.00  0.00           H  
HETATM   20  H5  UNL     1       5.889  -0.989   0.573  1.00  0.00           H  
HETATM   21  H6  UNL     1       3.763  -1.880  -0.398  1.00  0.00           H  
HETATM   22  H7  UNL     1       3.595  -0.983   1.127  1.00  0.00           H  
HETATM   23  H8  UNL     1       3.152   0.007  -1.755  1.00  0.00           H  
HETATM   24  H9  UNL     1       2.880   1.062  -0.355  1.00  0.00           H  
HETATM   25  H10 UNL     1       1.324  -1.434  -1.185  1.00  0.00           H  
HETATM   26  H11 UNL     1       0.846   0.287  -1.222  1.00  0.00           H  
HETATM   27  H12 UNL     1       1.117   0.416   1.262  1.00  0.00           H  
HETATM   28  H13 UNL     1       1.600  -1.300   1.315  1.00  0.00           H  
HETATM   29  H14 UNL     1      -0.702  -1.066   2.020  1.00  0.00           H  
HETATM   30  H15 UNL     1      -0.468  -2.124   0.612  1.00  0.00           H  
HETATM   31  H16 UNL     1      -1.470   0.781   0.696  1.00  0.00           H  
HETATM   32  H17 UNL     1      -1.755  -0.936  -1.530  1.00  0.00           H  
HETATM   33  H18 UNL     1      -2.921  -1.064   1.686  1.00  0.00           H  
HETATM   34  H19 UNL     1      -2.807  -1.927   0.141  1.00  0.00           H  
HETATM   35  H20 UNL     1      -3.921  -0.282  -1.108  1.00  0.00           H  
HETATM   36  H21 UNL     1      -4.925  -0.726   0.287  1.00  0.00           H  
HETATM   37  H22 UNL     1      -3.248   1.845   0.171  1.00  0.00           H  
HETATM   38  H23 UNL     1      -4.313   1.221   1.536  1.00  0.00           H  
HETATM   39  H24 UNL     1      -7.409   1.736   0.010  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3   19   20
CONECT    3    4   21   22
CONECT    4    5   23   24
CONECT    5    6   25   26
CONECT    6    7   27   28
CONECT    7    8   29   30
CONECT    8    9   10   31
CONECT    9   32
CONECT   10   11   33   34
CONECT   11   12   35   36
CONECT   12   13   37   38
CONECT   13   14   14   15
CONECT   15   39
END

HMDB0040169
     RDKit          3D
xi-5-Hydroxydodecanoic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.2944    1.0513    0.5691 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2228   -0.3299   -0.0383 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8073   -0.8770    0.0483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8550    0.0133   -0.6863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4230   -0.4824   -0.6388 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9450   -0.5644    0.7679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485   -1.0500    0.9178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5152   -0.2429    0.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4178   -0.1065   -1.0997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8450   -0.9176    0.6013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0040   -0.1943   -0.0052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1361    1.2331    0.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3111    1.8171   -0.2221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2159    2.2012   -1.4145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5059    1.9378    0.4604 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3187    1.1855    0.9917 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5804    1.1492    1.4142 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1353    1.8404   -0.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5897   -0.3076   -1.0682 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8890   -0.9887    0.5734 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7629   -1.8801   -0.3980 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5948   -0.9830    1.1270 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1523    0.0074   -1.7547 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8800    1.0621   -0.3550 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3243   -1.4341   -1.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8459    0.2869   -1.2224 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1175    0.4158    1.2618 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6001   -1.3001    1.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7023   -1.0664    2.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4679   -2.1236    0.6115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4697    0.7812    0.6957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7554   -0.9364   -1.5296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9209   -1.0644    1.6857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8067   -1.9270    0.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9213   -0.2823   -1.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9246   -0.7256    0.2873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2477    1.8447    0.1707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3135    1.2212    1.5360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4087    1.7361    0.0096 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  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 11 36  1  0
 12 37  1  0
 12 38  1  0
 15 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
XI-5-hydroxydodecanoate	Generator
5-Hydroxydecanoate	HMDB
5-Hydroxydecanoic acid sodium	HMDB

Chemical Formula

C₁₂H₂₄O₃

Average Molecular Weight

216.3172

Monoisotopic Molecular Weight

216.172544634

IUPAC Name

5-hydroxydodecanoic acid

Traditional Name

5-hydroxydodecanoic acid

CAS Registry Number

7779-95-5

SMILES

CCCCCCCC(O)CCCC(O)=O

InChI Identifier

InChI=1S/C12H24O3/c1-2-3-4-5-6-8-11(13)9-7-10-12(14)15/h11,13H,2-10H2,1H3,(H,14,15)

InChI Key

LXNOENXQFNYMGT-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Hydroxy fatty acid
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Organelle

Adiposome (HMDB: HMDB0040169)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0040169)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0040169)

Source

Endogenous

Endogenous (HMDB: HMDB0040169)

Animal

Animal (HMDB: HMDB0040169)

Exogenous

Food

Food (HMDB: HMDB0040169)

Milk and milk product

Milk and milk products (FooDB: FOOD00863)

Exogenous (HMDB: HMDB0040169)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0040169)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0040169)

Lipid metabolism pathway (HMDB: HMDB0040169)

Cellular process

Cell signaling (HMDB: HMDB0040169)

Biochemical process

Lipid transport (HMDB: HMDB0040169)

Role

Biological role

Energy source (HMDB: HMDB0040169)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0040169)

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	0.37 g/L	ALOGPS
logP	3.55	ALOGPS
logP	3.09	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	4.71	ChemAxon
pKa (Strongest Basic)	-1.2	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	10	ChemAxon
Refractivity	60.35 m³·mol⁻¹	ChemAxon
Polarizability	26.6 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]+	153.686	31661259
DarkChem	[M-H]-	151.431	31661259
DeepCCS	[M+H]+	152.539	30932474
DeepCCS	[M-H]-	148.514	30932474
DeepCCS	[M-2H]-	185.911	30932474
DeepCCS	[M+Na]+	161.596	30932474
AllCCS	[M+H]+	156.5	32859911
AllCCS	[M+H-H2O]+	153.0	32859911
AllCCS	[M+NH4]+	159.7	32859911
AllCCS	[M+Na]+	160.7	32859911
AllCCS	[M-H]-	156.0	32859911
AllCCS	[M+Na-2H]-	157.1	32859911
AllCCS	[M+HCOO]-	158.4	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.	7.21 minutes	32390414
Predicted by Siyang on May 30, 2022	12.9059 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.51 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	44.2 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2164.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	309.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	162.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	180.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	355.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	565.6 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	500.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	109.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1157.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	416.9 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	1353.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	350.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	339.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	439.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	256.9 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	91.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
xi-5-Hydroxydodecanoic acid	CCCCCCCC(O)CCCC(O)=O	2964.2	Standard polar	33892256
xi-5-Hydroxydodecanoic acid	CCCCCCCC(O)CCCC(O)=O	1678.9	Standard non polar	33892256
xi-5-Hydroxydodecanoic acid	CCCCCCCC(O)CCCC(O)=O	1762.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
xi-5-Hydroxydodecanoic acid,1TMS,isomer #1	CCCCCCCC(CCCC(=O)O)O[Si](C)(C)C	1819.1	Semi standard non polar	33892256
xi-5-Hydroxydodecanoic acid,1TMS,isomer #2	CCCCCCCC(O)CCCC(=O)O[Si](C)(C)C	1800.9	Semi standard non polar	33892256
xi-5-Hydroxydodecanoic acid,2TMS,isomer #1	CCCCCCCC(CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	1864.1	Semi standard non polar	33892256
xi-5-Hydroxydodecanoic acid,1TBDMS,isomer #1	CCCCCCCC(CCCC(=O)O)O[Si](C)(C)C(C)(C)C	2054.7	Semi standard non polar	33892256
xi-5-Hydroxydodecanoic acid,1TBDMS,isomer #2	CCCCCCCC(O)CCCC(=O)O[Si](C)(C)C(C)(C)C	2034.1	Semi standard non polar	33892256
xi-5-Hydroxydodecanoic acid,2TBDMS,isomer #1	CCCCCCCC(CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2310.6	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 - xi-5-Hydroxydodecanoic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-01bi-9500000000-ad1773be27b82df81560	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-5-Hydroxydodecanoic acid GC-MS (2 TMS) - 70eV, Positive	splash10-00fr-9142000000-23c44f188a84cf9ceb55	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-5-Hydroxydodecanoic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - xi-5-Hydroxydodecanoic 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 - xi-5-Hydroxydodecanoic acid 10V, Positive-QTOF	splash10-0002-0910000000-9dcefa574b0df61bc1f7	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 20V, Positive-QTOF	splash10-0002-5900000000-ab1ed706b74fa4afc1b6	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 40V, Positive-QTOF	splash10-0006-9200000000-57beaa3cde6f421891d0	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 10V, Negative-QTOF	splash10-014i-0590000000-3bca03ff5aa2b2e70c6a	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 20V, Negative-QTOF	splash10-00kb-2940000000-5bdadc0befe0b12ec858	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 40V, Negative-QTOF	splash10-052g-9400000000-eea20377b61c578878fe	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 10V, Positive-QTOF	splash10-0002-4910000000-dfcc2f4eb85744dd8659	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 20V, Positive-QTOF	splash10-0ab9-9300000000-586d68f7d3dcf8638bc8	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 40V, Positive-QTOF	splash10-052f-9000000000-6ebd5841f6c87576ffc7	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 10V, Negative-QTOF	splash10-014i-0190000000-d6a838a966a9f74f4b3b	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 20V, Negative-QTOF	splash10-014j-7790000000-233608bc683eb6873341	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - xi-5-Hydroxydodecanoic acid 40V, Negative-QTOF	splash10-052g-9700000000-bf39f7afb240f2565131	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

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

FDB019878

KNApSAcK ID

Not Available

Chemspider ID

22928

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24520

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 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for xi-5-Hydroxydodecanoic acid (HMDB0040169)

MOL for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

3D MOL for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

3D SDF for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

3D-SDF for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

PDB for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

3D PDB for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

SMILES for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

INCHI for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

Structure for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

3D Structure for HMDB0040169 (xi-5-Hydroxydodecanoic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra