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Showing metabocard for (R)-3-Hydroxyhexanoic acid (HMDB0010718)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-10-15 12:12:16 UTC
Update Date2023-02-21 17:17:25 UTC
HMDB IDHMDB0010718
Secondary Accession Numbers
  • HMDB10718
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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0010718 ((R)-3-Hydroxyhexanoic acid)

  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
Download

3D MOL for HMDB0010718 ((R)-3-Hydroxyhexanoic acid)

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 HMDB0010718 ((R)-3-Hydroxyhexanoic acid)

  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>
HMDB0010718

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0010718 ((R)-3-Hydroxyhexanoic acid)

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 HMDB0010718 ((R)-3-Hydroxyhexanoic acid)

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 HMDB0010718 ((R)-3-Hydroxyhexanoic acid)

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 HMDB0010718 ((R)-3-Hydroxyhexanoic acid)

CCC[C@@H](O)CC(O)=O
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INCHI for HMDB0010718 ((R)-3-Hydroxyhexanoic acid)

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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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC6H12O3
Average Molecular Weight132.1577
Monoisotopic Molecular Weight132.07864425
IUPAC Name(3R)-3-hydroxyhexanoic acid
Traditional Name3R-hydroxy-hexanoic acid
CAS Registry Number77877-35-1
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
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
Source
Process
Naturally occurring process
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB027868
KNApSAcK IDNot Available
Chemspider ID8373213
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10197713
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available