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Showing metabocard for 2-Hydroxycaproic acid (HMDB0001624)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-20 22:13:12 UTC
Update Date2023-02-21 17:15:48 UTC
HMDB IDHMDB0001624
Secondary Accession Numbers
  • HMDB01624
Metabolite Identification
Common Name2-Hydroxycaproic acid
Description2-hydroxycaproic acid, also known as 2-hydroxyhexanoic acid is a hydroxy fatty acid that is caproic (hexanoic) acid substituted by a hydroxy group at position 2. It has a role as an animal metabolite. It derives from a hexanoic acid. It is a conjugate acid of a 2-hydroxyhexanoate. 2-hydroxycaproic acid is a branched-chain alpha-keto acid that have been reported in normal human blood (PMID:7130306 ) and in normal amniotic fluid (PMID:7076774 ). It has been found that 2-hydroxycaproic acid is the most significant metabolite found in the CSF of patients infected with Nocardia. Nocardia sp. is an uncommon cause of meningitis, and Nocardia meningitis has a clinical picture similar to that of tuberculous meningitis (PMID:3818936 ; PMID:20615997 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001624 (2-Hydroxycaproic acid)

  Mrv1652305261923542D          

  9  8  0  0  0  0            999 V2000
   11.7455   -6.3450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7455   -5.5184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.4565   -6.7560    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0306   -6.7603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3153   -6.3492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8852   -6.3535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6004   -6.7645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1744   -6.7645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0309   -7.4534    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  6  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
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3D MOL for HMDB0001624 (2-Hydroxycaproic acid)

HMDB0001624
     RDKit          3D
2-Hydroxycaproic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.4443    0.6558    1.1477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2550   -0.5450    0.2396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9033   -0.4118   -0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2268   -0.3744    0.5924 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4975   -0.2373   -0.2632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3607    0.9375   -0.9724 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7083   -0.2993    0.5552 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9282   -1.3254    1.2399 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6193    0.7416    0.5965 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7047    1.4669    0.9199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4444    1.1361    0.9831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3487    0.2913    2.1821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0114   -0.4468   -0.5661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4151   -1.5014    0.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9112    0.5332   -0.9867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6843   -1.2260   -1.1287 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2891   -1.3145    1.1787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2053    0.4991    1.2434 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4238   -1.1115   -0.9756 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1363    1.1846   -1.5069 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7271    1.3473   -0.2040 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
  5  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  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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3D SDF for HMDB0001624 (2-Hydroxycaproic acid)

  Mrv1652305261923542D          

  9  8  0  0  0  0            999 V2000
   11.7455   -6.3450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7455   -5.5184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.4565   -6.7560    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0306   -6.7603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3153   -6.3492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8852   -6.3535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6004   -6.7645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1744   -6.7645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0309   -7.4534    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  6  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001624

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC(O)C(O)=O

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

> <INCHI_KEY>
NYHNVHGFPZAZGA-UHFFFAOYSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.1577

> <EXACT_MASS>
132.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.038583760539314

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxyhexanoic acid

> <ALOGPS_LOGP>
0.86

> <JCHEM_LOGP>
0.939830207

> <ALOGPS_LOGS>
-0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.284162726812554

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.257947363146006

> <JCHEM_PKA_STRONGEST_BASIC>
-3.797522654160839

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.565799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.85e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
hydroxyhexanoate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001624 (2-Hydroxycaproic acid)

HMDB0001624
     RDKit          3D
2-Hydroxycaproic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.4443    0.6558    1.1477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2550   -0.5450    0.2396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9033   -0.4118   -0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2268   -0.3744    0.5924 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4975   -0.2373   -0.2632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3607    0.9375   -0.9724 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7083   -0.2993    0.5552 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9282   -1.3254    1.2399 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6193    0.7416    0.5965 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7047    1.4669    0.9199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4444    1.1361    0.9831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3487    0.2913    2.1821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0114   -0.4468   -0.5661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4151   -1.5014    0.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9112    0.5332   -0.9867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6843   -1.2260   -1.1287 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2891   -1.3145    1.1787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2053    0.4991    1.2434 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4238   -1.1115   -0.9756 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1363    1.1846   -1.5069 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7271    1.3473   -0.2040 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
  5  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  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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PDB for HMDB0001624 (2-Hydroxycaproic acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0      21.925 -11.844   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      21.925 -10.301   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      23.252 -12.611   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      20.590 -12.619   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      19.255 -11.852   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.586 -11.860   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.921 -12.627   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.259 -12.627   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      20.591 -13.913   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5    9                                                  
CONECT    5    4    7                                                       
CONECT    6    7    8                                                       
CONECT    7    5    6                                                       
CONECT    8    6                                                            
CONECT    9    4                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0001624 (2-Hydroxycaproic acid)

COMPND    HMDB0001624
HETATM    1  C1  UNL     1      -2.444   0.656   1.148  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.255  -0.545   0.240  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.903  -0.412  -0.408  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.227  -0.374   0.592  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.498  -0.237  -0.263  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.361   0.938  -0.972  1.00  0.00           O  
HETATM    7  C6  UNL     1       2.708  -0.299   0.555  1.00  0.00           C  
HETATM    8  O2  UNL     1       2.928  -1.325   1.240  1.00  0.00           O  
HETATM    9  O3  UNL     1       3.619   0.742   0.597  1.00  0.00           O  
HETATM   10  H1  UNL     1      -1.705   1.467   0.920  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.444   1.136   0.983  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.349   0.291   2.182  1.00  0.00           H  
HETATM   13  H4  UNL     1      -3.011  -0.447  -0.566  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.415  -1.501   0.743  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.911   0.533  -0.987  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.684  -1.226  -1.129  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.289  -1.314   1.179  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.205   0.499   1.243  1.00  0.00           H  
HETATM   19  H10 UNL     1       1.424  -1.111  -0.976  1.00  0.00           H  
HETATM   20  H11 UNL     1       2.136   1.185  -1.507  1.00  0.00           H  
HETATM   21  H12 UNL     1       3.727   1.347  -0.204  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6    7   19
CONECT    6   20
CONECT    7    8    8    9
CONECT    9   21
END
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SMILES for HMDB0001624 (2-Hydroxycaproic acid)

CCCCC(O)C(O)=O
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INCHI for HMDB0001624 (2-Hydroxycaproic acid)

InChI=1S/C6H12O3/c1-2-3-4-5(7)6(8)9/h5,7H,2-4H2,1H3,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H12O3
Average Molecular Weight132.1577
Monoisotopic Molecular Weight132.07864425
IUPAC Name2-hydroxyhexanoic acid
Traditional Namehydroxyhexanoate
CAS Registry Number6064-63-7
SMILES
CCCCC(O)C(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-2-3-4-5(7)6(8)9/h5,7H,2-4H2,1H3,(H,8,9)
InChI KeyNYHNVHGFPZAZGA-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Hydroxy fatty acid
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Monosaccharide
  • 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 locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point55 - 58 °CNot 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 Locations
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
UrineDetected and Quantified0.0 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022697
KNApSAcK IDNot Available
Chemspider ID90191
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6332
PubChem Compound99824
PDB IDNot Available
ChEBI ID86542
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceAbderhalden, Emil; Weil, Arthur. A New Amino Acid of the Composition C6H13NO3, Obtained by the Total Hydrolysis of Nerve Proteins. Z. physiol. Chem. (1913), 84 39-59.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Woolf LI, Hasinoff C, Perry A: Estimation of branched-chain alpha-keto acids in blood by gas chromatography. J Chromatogr. 1982 Sep 10;231(2):237-45. [PubMed:7130306 ]
  2. Ng KJ, Andresen BD, Bianchine JR, Iams JD, O'Shaugnessy RW, Stempel LE, Zuspan FP: Capillary gas chromatographic-mass spectrometric profiles of trimethylsilyl derivatives of organic acids from amniotic fluids of different gestational age. J Chromatogr. 1982 Mar 12;228:43-50. [PubMed:7076774 ]
  3. Brooks JB, Kasin JV, Fast DM, Daneshvar MI: Detection of metabolites by frequency-pulsed electron capture gas-liquid chromatography in serum and cerebrospinal fluid of a patient with Nocardia infection. J Clin Microbiol. 1987 Feb;25(2):445-8. [PubMed:3818936 ]
  4. van Duynhoven J, Vaughan EE, Jacobs DM, Kemperman RA, van Velzen EJ, Gross G, Roger LC, Possemiers S, Smilde AK, Dore J, Westerhuis JA, Van de Wiele T: Metabolic fate of polyphenols in the human superorganism. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4531-8. doi: 10.1073/pnas.1000098107. Epub 2010 Jun 25. [PubMed:20615997 ]