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Showing NP-Card for 2-Hydroxycaproic acid (NP0000577)

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Record Information
Version1.0
Created at2005-11-20 22:13:12 UTC
Updated at2021-06-29 00:47:08 UTC
NP-MRD IDNP0000577
Secondary Accession NumbersNone
Natural Product 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 NP0000577 (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 NP0000577 (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
Download

3D SDF for NP0000577 (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>
NP0000577

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000577 (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 NP0000577 (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 NP0000577 (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 NP0000577 (2-Hydroxycaproic acid)

CCCCC(O)C(O)=O
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INCHI for NP0000577 (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 JSmol
Synonyms
ValueSource
2-HydroxycaproateGenerator
2-HydroxyhexanoateHMDB
2-Hydroxyhexanoic acidHMDB
DL-2-HydroxycaproateHMDB
DL-2-Hydroxycaproic acidHMDB
DL-2-HydroxyhexanoateHMDB
DL-2-Hydroxyhexanoic acidHMDB
DL-2-Hydroxyhexanoic acidhydroxyhexanoateHMDB
DL-2-Hydroxyhexanoic acidhydroxyhexanoic acidHMDB
DL-HydroxycaproateHMDB
DL-Hydroxycaproic acidHMDB
Hydroxy-N-caproateHMDB
Hydroxy-N-caproic acidHMDB
HydroxycaproateHMDB
Hydroxycaproic acidHMDB
HydroxyhexanoateHMDB
Hydroxyhexanoic acidHMDB
DL-2-Hydroxy caproateHMDB
2-Hydroxycaproic acidChEBI
Chemical FormulaC6H12O3
Average Mass132.1577 Da
Monoisotopic Mass132.07864 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Aloe africanaLOTUS Database
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point55 - 58 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility88.5 g/LALOGPS
logP0.86ALOGPS
logP0.94ChemAxon
logS-0.17ALOGPS
pKa (Strongest Acidic)4.26ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.57 m³·mol⁻¹ChemAxon
Polarizability14.04 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001624
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDNot Available
References
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 ]
  5. Dove AD, Leisen J, Zhou M, Byrne JJ, Lim-Hing K, Webb HD, Gelbaum L, Viant MR, Kubanek J, Fernandez FM: Biomarkers of whale shark health: a metabolomic approach. PLoS One. 2012;7(11):e49379. doi: 10.1371/journal.pone.0049379. Epub 2012 Nov 15. [PubMed:23166652 ]