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Showing NP-Card for 3-hydroxyhexanoic acid (NP0316404)

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Record Information
Version1.0
Created at2022-09-11 15:34:46 UTC
Updated at2022-09-11 15:34:46 UTC
NP-MRD IDNP0316404
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-hydroxyhexanoic acid
Description3-Hydroxyhexanoic acid, also known as 3-hydroxycaproate, 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. 3-Hydroxyhexanoic acid is a hydroxy fatty acid. 3-Hydroxyhexanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 3-hydroxyhexanoic acid is found in Solanum betaceum and Spondias mombin. In humans, 3-hydroxyhexanoic acid is involved in the metabolic disorder called the ethylmalonic encephalopathy pathway.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0316404 (3-hydroxyhexanoic acid)


  Mrv0541 04111415162D          

  9  8  0  0  0  0            999 V2000
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
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3D MOL for NP0316404 (3-hydroxyhexanoic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
    3.0028    0.1188   -0.1412 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5187    0.3988   -0.4270 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7650   -0.3129    0.6746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7178   -0.1578    0.5658 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0916    1.1732    0.6265 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3214   -0.7553   -0.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7762   -0.5052   -0.5986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5729   -1.4076   -0.9236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2804    0.7029   -0.1736 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2061   -0.9279   -0.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1088    0.2488    0.9751 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6290    0.8320   -0.6806 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3126    0.0024   -1.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3350    1.4851   -0.3750 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0507    0.1605    1.6576 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0696   -1.3635    0.7722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2087   -0.6873    1.4240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8514    1.5825   -0.2370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0953   -1.8550   -0.7717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8681   -0.3001   -1.5987 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2146    1.5676   -0.6601 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  9  1  0
  7  8  2  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  1
  5 18  1  0
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
Download

3D SDF for NP0316404 (3-hydroxyhexanoic acid)


  Mrv0541 04111415162D          

  9  8  0  0  0  0            999 V2000
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0316404

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCC(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)

> <INCHI_KEY>
HPMGFDVTYHWBAG-UHFFFAOYSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.1577

> <EXACT_MASS>
132.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
14.016104977971409

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
32.589099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.33e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxyhexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0316404 (3-hydroxyhexanoic acid)

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PDB for NP0316404 (3-hydroxyhexanoic acid)
HEADER    PROTEIN                                 11-APR-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-APR-14         0                                  
HETATM    1  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    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 NP0316404 (3-hydroxyhexanoic acid)
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SMILES for NP0316404 (3-hydroxyhexanoic acid)
CCCC(O)CC(O)=O
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INCHI for NP0316404 (3-hydroxyhexanoic acid)
InChI=1S/C6H12O3/c1-2-3-5(7)4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)
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View in JSmol
Synonyms
ValueSource
3-Hydroxycaproic acidChEBI
3-HydroxycaproateGenerator
3-HydroxyhexanoateGenerator
DL-3-Hydroxy caproateHMDB
Chemical FormulaC6H12O3
Average Mass132.1577 Da
Monoisotopic Mass132.07864 Da
IUPAC Name3-hydroxyhexanoic acid
Traditional Name3-hydroxyhexanoic acid
CAS Registry NumberNot Available
SMILES
CCCC(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)
InChI KeyHPMGFDVTYHWBAG-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cyphomandra betaceaLOTUS Database
Spondias mombinLOTUS Database
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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.57ALOGPS
logP0.58ChemAxon
logS0ALOGPS
pKa (Strongest Acidic)4.67ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.59 m³·mol⁻¹ChemAxon
Polarizability14.02 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0061652  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound151492  
PDB IDNot Available
ChEBI ID37035  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]