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Showing NP-Card for 6-hydroxyhexanoic acid (NP0305828)

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Record Information
Version1.0
Created at2022-09-10 21:56:38 UTC
Updated at2022-09-10 21:56:38 UTC
NP-MRD IDNP0305828
Secondary Accession NumbersNone
Natural Product Identification
Common Name6-hydroxyhexanoic acid
Description6-Hydroxyhexanoic acid, also known as 6-hydroxy caproate or 5-carboxypentanol, 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. 6-Hydroxyhexanoic acid was identified as the immediate product of hexanoate w-hydroxylation by whole cells and was further oxidized into adipic acid and an unexpected metabolite identified as 2-tetrahydrofuranacetic acid. 6-Hydroxyhexanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 6-Hydroxyhexanoic acid exists in all living organisms, ranging from bacteria to humans. Similar observations were made with 1,6-hexanediol serving as the carbon source and cells obtained from one organism,Pseudomonas aeruginosa PAO, grown either on 1,6-hexanediol or 6-hydroxyhexanoate,were found to be well induced for both 6-oxohexanoate and adipate oxidation. This same metabolite, together with adipic acid, was also detected when similarly induced cells were incubated with hexanoate or 1,6-hexanediol, but not with 6-oxohexanoate (adipic semialdehyde). 6-hydroxyhexanoic acid is found in Homo sapiens. It was first documented in 1983 (PMID: 6630146). Cells grown on hexanoate and incubated with 6-Hydroxyhexanoic acid were also found to accumulate 2-tetrahydrofuranacetic acid, which was not further degraded (PMID: 14698179).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0305828 (6-hydroxyhexanoic acid)


  Mrv1652303102016462D          

  9  8  0  0  0  0            999 V2000
   11.7081  -15.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1206  -14.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8831  -15.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9456  -14.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4707  -15.9041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3580  -13.7611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6457  -15.9041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1830  -13.7611    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9456  -13.0465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  2  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
M  END
Download

3D MOL for NP0305828 (6-hydroxyhexanoic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.0445   -1.5386    0.8872 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3899   -0.5649    0.4263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5813    0.7156    0.8655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3934   -0.8716   -0.6236 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5880    0.2995   -1.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2373    0.9587   -0.0101 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2517    0.0464    0.6198 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2352   -0.5083   -0.3649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9354    0.5354   -0.9789 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4823    0.9288    1.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7421   -1.7340   -0.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9966   -1.2634   -1.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2688    1.0594   -1.5273 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0874   -0.0590   -1.8932 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8111    1.7804   -0.5202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3897    1.4058    0.7810 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8203    0.6413    1.3665 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7369   -0.7872    1.1461 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7707   -1.1559   -1.1296 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9545   -1.1374    0.1980 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0362    1.2491   -0.3006 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  9 21  1  0
  8 19  1  0
  8 20  1  0
  7 17  1  0
  7 18  1  0
  6 15  1  0
  6 16  1  0
  5 13  1  0
  5 14  1  0
  4 11  1  0
  4 12  1  0
  3 10  1  0
M  END
Download

3D SDF for NP0305828 (6-hydroxyhexanoic acid)


  Mrv1652303102016462D          

  9  8  0  0  0  0            999 V2000
   11.7081  -15.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1206  -14.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8831  -15.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9456  -14.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4707  -15.9041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3580  -13.7611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6457  -15.9041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1830  -13.7611    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9456  -13.0465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  2  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0305828

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O3/c7-5-3-1-2-4-6(8)9/h7H,1-5H2,(H,8,9)

> <INCHI_KEY>
IWHLYPDWHHPVAA-UHFFFAOYSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.1577

> <EXACT_MASS>
132.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.243634575644695

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-hydroxyhexanoic acid

> <ALOGPS_LOGP>
0.29

> <JCHEM_LOGP>
0.37421751100000017

> <ALOGPS_LOGS>
-0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
16.843935536859917

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.710101883850394

> <JCHEM_PKA_STRONGEST_BASIC>
-1.9922627018970158

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
33.0023

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.97e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-hydroxyhexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0305828 (6-hydroxyhexanoic acid)

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PDB for NP0305828 (6-hydroxyhexanoic acid)
HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0      21.855 -28.354   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      22.625 -27.020   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      20.315 -28.354   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      24.165 -27.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      19.545 -29.688   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      24.935 -25.687   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      18.005 -29.688   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      26.475 -25.687   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      24.165 -24.353   0.000  0.00  0.00           O+0
CONECT    1    3    2                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    8    9                                                  
CONECT    7    5                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0305828 (6-hydroxyhexanoic acid)
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SMILES for NP0305828 (6-hydroxyhexanoic acid)
OCCCCCC(O)=O
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INCHI for NP0305828 (6-hydroxyhexanoic acid)
InChI=1S/C6H12O3/c7-5-3-1-2-4-6(8)9/h7H,1-5H2,(H,8,9)
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View in JSmol
Synonyms
ValueSource
5-CarboxypentanolChEBI
5-Hydroxypentanecarboxylic acidChEBI
6-Hydroxy caproic acidChEBI
6-Hydroxycaproic acidChEBI
6-HydroxyhexanoateChEBI
epsilon-Hydroxycaproic acidChEBI
epsilon-Hydroxyhexanoic acidChEBI
5-HydroxypentanecarboxylateGenerator
6-Hydroxy caproateGenerator
6-HydroxycaproateGenerator
epsilon-HydroxycaproateGenerator
epsilon-HydroxyhexanoateGenerator
6-Hydroxyhexanoic acidGenerator
Chemical FormulaC6H12O3
Average Mass132.1577 Da
Monoisotopic Mass132.07864 Da
IUPAC Name6-hydroxyhexanoic acid
Traditional Name6-hydroxyhexanoic acid
CAS Registry NumberNot Available
SMILES
OCCCCCC(O)=O
InChI Identifier
InChI=1S/C6H12O3/c7-5-3-1-2-4-6(8)9/h7H,1-5H2,(H,8,9)
InChI KeyIWHLYPDWHHPVAA-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
Homo sapiensLOTUS 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
    • 

  • Hydroxy fatty acid
    • 

  • Straight chain fatty acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Primary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • 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
logP0.29ALOGPS
logP0.37ChemAxon
logS-0.28ALOGPS
pKa (Strongest Acidic)4.71ChemAxon
pKa (Strongest Basic)-2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity33 m³·mol⁻¹ChemAxon
Polarizability14.24 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0012843  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029184  
KNApSAcK IDNot Available
Chemspider ID13835  
KEGG Compound IDC06103  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14490  
PDB IDNot Available
ChEBI ID17869  
Good Scents IDNot Available
References
General References
  1. Wu TY, Hassig C, Wu Y, Ding S, Schultz PG: Design, synthesis, and activity of HDAC inhibitors with a N-formyl hydroxylamine head group. Bioorg Med Chem Lett. 2004 Jan 19;14(2):449-53. doi: 10.1016/j.bmcl.2003.10.055. [PubMed:14698179  ] 
  2. Kunz DA, Weimer PJ: Bacterial formation and metabolism of 6-hydroxyhexanoate: evidence of a potential role for omega-oxidation. J Bacteriol. 1983 Nov;156(2):567-75. doi: 10.1128/jb.156.2.567-575.1983. [PubMed:6630146  ] 
  3. LOTUS database [Link]