Showing metabocard for (R)-3-Hydroxyhexanoic acid (MMDBc0047805)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 15:43:31 UTC
Update Date2022-09-01 01:59:23 UTC
Metabolite IDMMDBc0047805
Metabolite Identification
Common Name(R)-3-Hydroxyhexanoic acid
Description(R)-3-Hydroxyhexanoic acid, also known as D-beta-hydroxycaproate or D-β-hydroxycaproic acid, belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain (R)-3-Hydroxyhexanoic acid exists in all eukaryotes, ranging from yeast to plants to humans. In humans, (R)-3-hydroxyhexanoic acid is involved in the fatty acid biosynthesis pathway (R)-3-Hydroxyhexanoic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make (R)-3-hydroxyhexanoic acid a potential biomarker for the consumption of these foods (R)-3-Hydroxyhexanoic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on (R)-3-Hydroxyhexanoic acid.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fecf0dea208>


  Mrv1652310241917282D          

  9  8  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  2  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
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  1  6  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
M  END
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3D MOL for #<Metabolite:0x00007fecf0dea208>

HMDB0010718
     RDKit          3D
(R)-3-Hydroxyhexanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.1292   -0.4452    0.2308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9252   -0.0823   -0.6086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6983   -0.1882    0.2569 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5690    0.1743   -0.4878 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5405    1.4632   -0.9665 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7328    0.0161    0.4494 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0187    0.3557   -0.2093 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1504    1.4908   -0.7292 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0815   -0.5330   -0.2684 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7982   -0.8665    1.2148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7485    0.4454    0.4669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7545   -1.2274   -0.2741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8657   -0.7393   -1.4986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9876    0.9982   -0.9153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5920   -1.1903    0.7311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8078    0.5710    1.0749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7019   -0.5126   -1.3745 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2535    2.0815   -0.2334 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5759    0.7250    1.2948 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7763   -1.0001    0.8801 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9065   -1.5364   -0.3560 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
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  6
  5 18  1  0
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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3D SDF for #<Metabolite:0x00007fecf0dea208>


  Mrv1652310241917282D          

  9  8  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  2  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
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  1  6  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
M  END
> <DATABASE_ID>
MMDBc0047805

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O3/c1-2-3-5(7)4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m1/s1

> <INCHI_KEY>
HPMGFDVTYHWBAG-RXMQYKEDSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.1577

> <EXACT_MASS>
132.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.870108062232962

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.57

> <JCHEM_LOGP>
0.5800850606666665

> <ALOGPS_LOGS>
0.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.288991049395367

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.67423988970905

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7983718893851792

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.5891

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.33e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3R-hydroxy-hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fecf0dea208>

HMDB0010718
     RDKit          3D
(R)-3-Hydroxyhexanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.1292   -0.4452    0.2308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9252   -0.0823   -0.6086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6983   -0.1882    0.2569 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5690    0.1743   -0.4878 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5405    1.4632   -0.9665 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7328    0.0161    0.4494 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0187    0.3557   -0.2093 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1504    1.4908   -0.7292 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0815   -0.5330   -0.2684 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7982   -0.8665    1.2148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7485    0.4454    0.4669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7545   -1.2274   -0.2741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8657   -0.7393   -1.4986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9876    0.9982   -0.9153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5920   -1.1903    0.7311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8078    0.5710    1.0749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7019   -0.5126   -1.3745 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2535    2.0815   -0.2334 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5759    0.7250    1.2948 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7763   -1.0001    0.8801 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9065   -1.5364   -0.3560 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
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  6
  5 18  1  0
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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PDB for #<Metabolite:0x00007fecf0dea208>

HEADER    PROTEIN                                 24-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-OCT-19         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
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                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x00007fecf0dea208>

COMPND    HMDB0010718
HETATM    1  C1  UNL     1      -3.129  -0.445   0.231  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.925  -0.082  -0.609  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.698  -0.188   0.257  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.569   0.174  -0.488  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.541   1.463  -0.967  1.00  0.00           O  
HETATM    6  C5  UNL     1       1.733   0.016   0.449  1.00  0.00           C  
HETATM    7  C6  UNL     1       3.019   0.356  -0.209  1.00  0.00           C  
HETATM    8  O2  UNL     1       3.150   1.491  -0.729  1.00  0.00           O  
HETATM    9  O3  UNL     1       4.082  -0.533  -0.268  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.798  -0.867   1.215  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.749   0.445   0.467  1.00  0.00           H  
HETATM   12  H3  UNL     1      -3.754  -1.227  -0.274  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.866  -0.739  -1.499  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.988   0.998  -0.915  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.592  -1.190   0.731  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.808   0.571   1.075  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.702  -0.513  -1.374  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.254   2.081  -0.233  1.00  0.00           H  
HETATM   19  H10 UNL     1       1.576   0.725   1.295  1.00  0.00           H  
HETATM   20  H11 UNL     1       1.776  -1.000   0.880  1.00  0.00           H  
HETATM   21  H12 UNL     1       3.907  -1.536  -0.356  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4   15   16
CONECT    4    5    6   17
CONECT    5   18
CONECT    6    7   19   20
CONECT    7    8    8    9
CONECT    9   21
END
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SMILES for #<Metabolite:0x00007fecf0dea208>

CCC[C@@H](O)CC(O)=O
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INCHI for #<Metabolite:0x00007fecf0dea208>

InChI=1S/C6H12O3/c1-2-3-5(7)4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m1/s1
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Synonyms
ValueSource
(R)-3-HydroxyhexanoateGenerator
(3R)-3-HydroxyhexanoateHMDB
(3R)-3-Hydroxyhexanoic acidHMDB
(±)-3-hydroxyhexanoateHMDB
(±)-3-hydroxyhexanoic acidHMDB
3-HydroxycaproateHMDB
3-Hydroxycaproic acidHMDB
3-HydroxyhexanoateHMDB
3-Hydroxyhexanoic acidHMDB
D-beta-HydroxycaproateHMDB
D-beta-Hydroxycaproic acidHMDB
D-Β-hydroxycaproateHMDB
D-Β-hydroxycaproic acidHMDB
FA(6:0(3-OH))HMDB
FA(6:0(3R-OH))HMDB
beta-Hydroxy-N-caproateHMDB
beta-Hydroxy-N-caproic acidHMDB
beta-HydroxycaproateHMDB
beta-Hydroxycaproic acidHMDB
beta-HydroxyhexanoateHMDB
beta-Hydroxyhexanoic acidHMDB
Β-hydroxy-N-caproateHMDB
Β-hydroxy-N-caproic acidHMDB
Β-hydroxycaproateHMDB
Β-hydroxycaproic acidHMDB
Β-hydroxyhexanoateHMDB
Β-hydroxyhexanoic acidHMDB
(R)-3-Hydroxyhexanoic acidHMDB
Molecular FormulaC6H12O3
Average Mass132.1577
Monoisotopic Mass132.07864425
IUPAC Name(3R)-3-hydroxyhexanoic acid
Traditional Name3R-hydroxy-hexanoic acid
CAS Registry NumberNot Available
SMILES
CCC[C@@H](O)CC(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-2-3-5(7)4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m1/s1
InChI KeyHPMGFDVTYHWBAG-RXMQYKEDSA-N