Hmdb loader

Showing metabocard for 3-Hydroxyoctanoic acid (HMDB0001954)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:29 UTC
Update Date2023-02-21 17:15:59 UTC
HMDB IDHMDB0001954
Secondary Accession Numbers
  • HMDB01954
Metabolite Identification
Common Name3-Hydroxyoctanoic acid
Description3-Hydroxyoctanoic acid (CAS: 14292-27-4) is an organic 3-hydroxy dicarboxylic acid, a metabolite of medium-chain fatty acid oxidation found in human urine. It is believed that urinary 3-hydroxy dicarboxylic acids are derived from the omega-oxidation of 3-hydroxy fatty acids and the subsequent beta-oxidation of longer-chain 3-hydroxy dicarboxylic acids. (PMID:1870421 ). 3-Hydroxyoctanoic acid has been identified in the human placenta (PMID: 32033212 ).
Structure
Data?1676999759
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001954 (3-Hydroxyoctanoic acid)


  Mrv1652303062020142D          

 11 10  0  0  0  0            999 V2000
 9997.9637 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2489 9998.4815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9996.5339 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8190 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.1042 9998.0698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8190 9999.3071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2489 9999.3071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6785 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3942 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.1078 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.8234 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  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
M  END
Download

3D MOL for HMDB0001954 (3-Hydroxyoctanoic acid)

HMDB0001954
     RDKit          3D
3-Hydroxyoctanoic acid
 27 26  0  0  0  0  0  0  0  0999 V2000
   -3.3415    0.7146    0.1341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5244   -0.5180   -0.2146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3828   -0.1453   -1.1353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4571    0.8601   -0.4992 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1751    0.3819    0.7644 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0093   -0.8526    0.5962 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5611   -1.2297    1.8175 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1023   -0.7274   -0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0815    0.3261   -0.1104 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0133    1.0605    0.9059 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1489    0.5548   -0.9658 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4116    0.4596    0.2651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9976    1.1719    1.0874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2409    1.4324   -0.7049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2086   -1.2048   -0.7495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1609   -1.0275    0.7055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8691   -1.0664   -1.4554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8316    0.3396   -2.0266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1044    1.7407   -0.2214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2848    1.2567   -1.2077 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7112    1.2216    1.2272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6597    0.1283    1.4726 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -1.7011    0.2695 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3904   -1.7567    1.7161 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6423   -1.7128   -0.4220 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6881   -0.6334   -1.4514 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0245    0.9267   -0.6315 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
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  6
  7 24  1  0
  8 25  1  0
  8 26  1  0
 11 27  1  0
M  END
Download

3D SDF for HMDB0001954 (3-Hydroxyoctanoic acid)


  Mrv1652303062020142D          

 11 10  0  0  0  0            999 V2000
 9997.9637 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2489 9998.4815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9996.5339 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8190 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.1042 9998.0698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8190 9999.3071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2489 9999.3071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6785 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3942 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.1078 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.8234 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  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
M  END
> <DATABASE_ID>
HMDB0001954

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H16O3/c1-2-3-4-5-7(9)6-8(10)11/h7,9H,2-6H2,1H3,(H,10,11)/t7-/m0/s1

> <INCHI_KEY>
NDPLAKGOSZHTPH-ZETCQYMHSA-N

> <FORMULA>
C8H16O3

> <MOLECULAR_WEIGHT>
160.2108

> <EXACT_MASS>
160.109944378

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
17.974111503150823

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S)-3-hydroxyoctanoic acid

> <ALOGPS_LOGP>
1.44

> <JCHEM_LOGP>
1.4692223906666668

> <ALOGPS_LOGS>
-1.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.288498485482194

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.83879184641206

> <JCHEM_PKA_STRONGEST_BASIC>
-2.798587340234124

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
41.79109999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.36e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-3-hydroxyoctanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001954 (3-Hydroxyoctanoic acid)

HMDB0001954
     RDKit          3D
3-Hydroxyoctanoic acid
 27 26  0  0  0  0  0  0  0  0999 V2000
   -3.3415    0.7146    0.1341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5244   -0.5180   -0.2146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3828   -0.1453   -1.1353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4571    0.8601   -0.4992 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1751    0.3819    0.7644 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0093   -0.8526    0.5962 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5611   -1.2297    1.8175 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1023   -0.7274   -0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0815    0.3261   -0.1104 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0133    1.0605    0.9059 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1489    0.5548   -0.9658 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4116    0.4596    0.2651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9976    1.1719    1.0874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2409    1.4324   -0.7049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2086   -1.2048   -0.7495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1609   -1.0275    0.7055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8691   -1.0664   -1.4554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8316    0.3396   -2.0266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1044    1.7407   -0.2214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2848    1.2567   -1.2077 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7112    1.2216    1.2272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6597    0.1283    1.4726 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3574   -1.7011    0.2695 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3904   -1.7567    1.7161 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6423   -1.7128   -0.4220 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6881   -0.6334   -1.4514 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0245    0.9267   -0.6315 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
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  6
  7 24  1  0
  8 25  1  0
  8 26  1  0
 11 27  1  0
M  END
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PDB for HMDB0001954 (3-Hydroxyoctanoic acid)

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  C   UNK     0    8662.8668663.064   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8661.5318663.832   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8660.1978663.064   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8658.8628663.832   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8657.5288663.064   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8658.8628665.373   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8661.5318665.373   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8664.2008663.832   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8665.5368663.064   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8666.8688663.832   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8668.2048663.064   0.000  0.00  0.00           C+0
CONECT    1    2    8                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2                                                            
CONECT    8    1    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0001954 (3-Hydroxyoctanoic acid)

COMPND    HMDB0001954
HETATM    1  C1  UNL     1      -3.342   0.715   0.134  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.524  -0.518  -0.215  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.383  -0.145  -1.135  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.457   0.860  -0.499  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.175   0.382   0.764  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.009  -0.853   0.596  1.00  0.00           C  
HETATM    7  O1  UNL     1       1.561  -1.230   1.817  1.00  0.00           O  
HETATM    8  C7  UNL     1       2.102  -0.727  -0.408  1.00  0.00           C  
HETATM    9  C8  UNL     1       3.082   0.326  -0.110  1.00  0.00           C  
HETATM   10  O2  UNL     1       3.013   1.060   0.906  1.00  0.00           O  
HETATM   11  O3  UNL     1       4.149   0.555  -0.966  1.00  0.00           O  
HETATM   12  H1  UNL     1      -4.412   0.460   0.265  1.00  0.00           H  
HETATM   13  H2  UNL     1      -2.998   1.172   1.087  1.00  0.00           H  
HETATM   14  H3  UNL     1      -3.241   1.432  -0.705  1.00  0.00           H  
HETATM   15  H4  UNL     1      -3.209  -1.205  -0.750  1.00  0.00           H  
HETATM   16  H5  UNL     1      -2.161  -1.027   0.705  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.869  -1.066  -1.455  1.00  0.00           H  
HETATM   18  H7  UNL     1      -1.832   0.340  -2.027  1.00  0.00           H  
HETATM   19  H8  UNL     1      -1.104   1.741  -0.221  1.00  0.00           H  
HETATM   20  H9  UNL     1       0.285   1.257  -1.208  1.00  0.00           H  
HETATM   21  H10 UNL     1       0.711   1.222   1.227  1.00  0.00           H  
HETATM   22  H11 UNL     1      -0.660   0.128   1.473  1.00  0.00           H  
HETATM   23  H12 UNL     1       0.357  -1.701   0.270  1.00  0.00           H  
HETATM   24  H13 UNL     1       2.390  -1.757   1.716  1.00  0.00           H  
HETATM   25  H14 UNL     1       2.642  -1.713  -0.422  1.00  0.00           H  
HETATM   26  H15 UNL     1       1.688  -0.633  -1.451  1.00  0.00           H  
HETATM   27  H16 UNL     1       5.024   0.927  -0.632  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3   15   16
CONECT    3    4   17   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7    8   23
CONECT    7   24
CONECT    8    9   25   26
CONECT    9   10   10   11
CONECT   11   27
END
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SMILES for HMDB0001954 (3-Hydroxyoctanoic acid)

CCCCC[C@H](O)CC(O)=O
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INCHI for HMDB0001954 (3-Hydroxyoctanoic acid)

InChI=1S/C8H16O3/c1-2-3-4-5-7(9)6-8(10)11/h7,9H,2-6H2,1H3,(H,10,11)/t7-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(3S)-3-Hydroxy-octanoic acidChEBI
(S)-3-Hydroxycaprylic acidChEBI
(S)-3-OH Octanoic acidChEBI
(S)-3-OH-Caprylic acidChEBI
(S)-beta-Hydroxycaprylic acidChEBI
(S)-beta-Hydroxyoctanoic acidChEBI
(S)-beta-OH-Caprylic acidChEBI
(S)-beta-OH-Octanoic acidChEBI
(3S)-3-Hydroxy-octanoateGenerator
(S)-3-HydroxycaprylateGenerator
(S)-3-OH OctanoateGenerator
(S)-3-OH-CaprylateGenerator
(S)-b-HydroxycaprylateGenerator
(S)-b-Hydroxycaprylic acidGenerator
(S)-beta-HydroxycaprylateGenerator
(S)-Β-hydroxycaprylateGenerator
(S)-Β-hydroxycaprylic acidGenerator
(S)-b-HydroxyoctanoateGenerator
(S)-b-Hydroxyoctanoic acidGenerator
(S)-beta-HydroxyoctanoateGenerator
(S)-Β-hydroxyoctanoateGenerator
(S)-Β-hydroxyoctanoic acidGenerator
(S)-b-OH-CaprylateGenerator
(S)-b-OH-Caprylic acidGenerator
(S)-beta-OH-CaprylateGenerator
(S)-Β-OH-caprylateGenerator
(S)-Β-OH-caprylic acidGenerator
(S)-b-OH-OctanoateGenerator
(S)-b-OH-Octanoic acidGenerator
(S)-beta-OH-OctanoateGenerator
(S)-Β-OH-octanoateGenerator
(S)-Β-OH-octanoic acidGenerator
3-HydroxyoctanoateGenerator
(S)-3-HydroxyoctanoateHMDB
3-Hydroxyoctanoic acid, (S)-isomerHMDB
(3S)-3-HydroxyoctanoateHMDB
(3S)-3-Hydroxyoctanoic acidHMDB
(±)-3-hydroxyoctanoateHMDB
(±)-3-hydroxyoctanoic acidHMDB
3-HydroxycaprylateHMDB
3-Hydroxycaprylic acidHMDB
FA(8:0(3-OH))HMDB
FA(8:0(3S-OH))HMDB
S-3-HydroxyoctanoateHMDB
S-3-Hydroxyoctanoic acidHMDB
beta-HydroxycaprylateHMDB
beta-Hydroxycaprylic acidHMDB
beta-HydroxyoctanoateHMDB
beta-Hydroxyoctanoic acidHMDB
Β-hydroxycaprylateHMDB
Β-hydroxycaprylic acidHMDB
Β-hydroxyoctanoateHMDB
Β-hydroxyoctanoic acidHMDB
3-Hydroxyoctanoic acidMeSH
Chemical FormulaC8H16O3
Average Molecular Weight160.2108
Monoisotopic Molecular Weight160.109944378
IUPAC Name(3S)-3-hydroxyoctanoic acid
Traditional Name(S)-3-hydroxyoctanoic acid
CAS Registry Number33796-86-0
SMILES
CCCCC[C@H](O)CC(O)=O
InChI Identifier
InChI=1S/C8H16O3/c1-2-3-4-5-7(9)6-8(10)11/h7,9H,2-6H2,1H3,(H,10,11)/t7-/m0/s1
InChI KeyNDPLAKGOSZHTPH-ZETCQYMHSA-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassMedium-chain hydroxy acids and derivatives
Direct ParentMedium-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 FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility13.6 g/LALOGPS
logP1.44ALOGPS
logP1.47ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)4.84ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity41.79 m³·mol⁻¹ChemAxon
Polarizability17.97 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+136.11830932474
DeepCCS[M-H]-132.28430932474
DeepCCS[M-2H]-169.40230932474
DeepCCS[M+Na]+144.96230932474
AllCCS[M+H]+139.632859911
AllCCS[M+H-H2O]+135.732859911
AllCCS[M+NH4]+143.332859911
AllCCS[M+Na]+144.432859911
AllCCS[M-H]-137.532859911
AllCCS[M+Na-2H]-139.432859911
AllCCS[M+HCOO]-141.632859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.4.21 minutes32390414
Predicted by Siyang on May 30, 202210.5977 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.41 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid81.4 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1508.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid296.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid121.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid181.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid163.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid409.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid416.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)103.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid828.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid333.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1147.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid250.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid288.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate455.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA192.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water124.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Hydroxyoctanoic acidCCCCC[C@H](O)CC(O)=O2430.1Standard polar33892256
3-Hydroxyoctanoic acidCCCCC[C@H](O)CC(O)=O1296.0Standard non polar33892256
3-Hydroxyoctanoic acidCCCCC[C@H](O)CC(O)=O1367.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Hydroxyoctanoic acid,1TMS,isomer #1CCCCC[C@@H](CC(=O)O)O[Si](C)(C)C1378.0Semi standard non polar33892256
3-Hydroxyoctanoic acid,1TMS,isomer #2CCCCC[C@H](O)CC(=O)O[Si](C)(C)C1382.0Semi standard non polar33892256
3-Hydroxyoctanoic acid,2TMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C)O[Si](C)(C)C1471.9Semi standard non polar33892256
3-Hydroxyoctanoic acid,1TBDMS,isomer #1CCCCC[C@@H](CC(=O)O)O[Si](C)(C)C(C)(C)C1601.6Semi standard non polar33892256
3-Hydroxyoctanoic acid,1TBDMS,isomer #2CCCCC[C@H](O)CC(=O)O[Si](C)(C)C(C)(C)C1616.6Semi standard non polar33892256
3-Hydroxyoctanoic acid,2TBDMS,isomer #1CCCCC[C@@H](CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C1923.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - 3-Hydroxyoctanoic acid GC-MS (2 TMS)splash10-00ov-5920000000-2c7ce12b4e2e186a597f2019-10-24HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 3-Hydroxyoctanoic acid GC-MS (Non-derivatized)splash10-00ov-5920000000-2c7ce12b4e2e186a597f2019-10-24HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyoctanoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyoctanoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyoctanoic acid 10V, Negative-QTOFsplash10-0a4i-4900000000-fd08cd8b97f656038b552021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyoctanoic acid 20V, Negative-QTOFsplash10-0a4i-9100000000-ad1d87402b7f1e5891722021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyoctanoic acid 40V, Negative-QTOFsplash10-0006-9000000000-191e4c2a7ad7ea5541dd2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyoctanoic acid 10V, Positive-QTOFsplash10-0odj-9500000000-95cc4658f3be66a2d9aa2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyoctanoic acid 20V, Positive-QTOFsplash10-0006-9000000000-2701ee861eb39af896352021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyoctanoic acid 40V, Positive-QTOFsplash10-0006-9000000000-e9a7bc1b045535fb0dbb2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified20 uMAdult (>18 years old)MaleNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified3-2400 uMChildren (1-13 years old)Male3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease References
3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency
  1. Thompson GN, Hsu BY, Pitt JJ, Treacy E, Stanley CA: Fasting hypoketotic coma in a child with deficiency of mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase. N Engl J Med. 1997 Oct 23;337(17):1203-7. doi: 10.1056/NEJM199710233371704. [PubMed:9337379 ]
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
  • 605911 (3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency)
  • 114500 (Colorectal cancer)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022761
KNApSAcK IDNot Available
Chemspider ID9542083
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Hydroxyoctanoic acid
METLIN IDNot Available
PubChem Compound11367166
PDB IDNot Available
ChEBI ID37100
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceTahara, Satoshi; Suzuki, Yumiko; Mizutani, Junya. Fungal metabolism of a,b-unsaturated carboxylic acids. Part III. Fungal metabolism of trans-2-octenoic acid. Agricultural and Biological Chemistry (1977), 41(9), 1643-50.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Bennett MJ, Ragni MC, Hood I, Hale DE: Comparison of post-mortem urinary and vitreous humour organic acids. Ann Clin Biochem. 1992 Sep;29 ( Pt 5):541-5. [PubMed:1444166 ]
  2. Tserng KY, Jin SJ, Kerr DS, Hoppel CL: Urinary 3-hydroxydicarboxylic acids in pathophysiology of metabolic disorders with dicarboxylic aciduria. Metabolism. 1991 Jul;40(7):676-82. [PubMed:1870421 ]
  3. Jones PM, Butt Y, Bennett MJ: Accumulation of 3-hydroxy-fatty acids in the culture medium of long-chain L-3-hydroxyacyl CoA dehydrogenase (LCHAD) and mitochondrial trifunctional protein-deficient skin fibroblasts: implications for medium chain triglyceride dietary treatment of LCHAD deficiency. Pediatr Res. 2003 May;53(5):783-7. Epub 2003 Mar 5. [PubMed:12621125 ]
  4. Montgomery JA, Mamer OA, Colle E: Profiles in altered metabolism. IV--Induction of acute dicarboxylic aciduria following 2-octynoic acid administration to the rat. Biomed Environ Mass Spectrom. 1989 Jun;18(6):416-23. [PubMed:2765701 ]
  5. Kelley RI, Morton DH: 3-Hydroxyoctanoic aciduria: identification of a new organic acid in the urine of a patient with non-ketotic hypoglycemia. Clin Chim Acta. 1988 Jun 30;175(1):19-26. [PubMed:3168281 ]
  6. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]