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Showing metabocard for 3-hydroxynona-4,6-dienoic acid (HMDB0341036)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2022-07-09 02:52:53 UTC
Update Date2022-07-09 02:52:53 UTC
HMDB IDHMDB0341036
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-hydroxynona-4,6-dienoic acid
Description3-hydroxynona-4,6-dienoic 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. In humans, 3-hydroxynona-4,6-dienoic acid is involved in the acylcarnitine 3-hydroxynona-4,6-dienoylcarnitine pathway. 3-hydroxynona-4,6-dienoic 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 3-hydroxynona-4,6-dienoic acid.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341036 (3-hydroxynona-4,6-dienoic acid)


  Mrv1652304102105242D          

 12 11  0  0  0  0            999 V2000
    4.5375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  5  1  4  0  0  0
  7  8  2  0  0  0  0
  9  8  1  4  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
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3D MOL for HMDB0341036 (3-hydroxynona-4,6-dienoic acid)

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3D SDF for HMDB0341036 (3-hydroxynona-4,6-dienoic acid)

  Mrv1652304102105242D          

 12 11  0  0  0  0            999 V2000
    4.5375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  5  1  4  0  0  0
  7  8  2  0  0  0  0
  9  8  1  4  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341036

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC=CC=CC(O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14O3/c1-2-3-4-5-6-8(10)7-9(11)12/h3-6,8,10H,2,7H2,1H3,(H,11,12)

> <INCHI_KEY>
DXBPYWYTZPHKMA-UHFFFAOYSA-N

> <FORMULA>
C9H14O3

> <MOLECULAR_WEIGHT>
170.208

> <EXACT_MASS>
170.094294311

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
18.734310671344563

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxynona-4,6-dienoic acid

> <ALOGPS_LOGP>
1.33

> <JCHEM_LOGP>
1.345855202333333

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.913435012910941

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.760615359038597

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9626086076900204

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
48.4713

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.31e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxynona-4,6-dienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341036 (3-hydroxynona-4,6-dienoic acid)
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PDB for HMDB0341036 (3-hydroxynona-4,6-dienoic acid)
HEADER    PROTEIN                                 10-APR-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-APR-21         0                                  
HETATM    1  O   UNK     0       8.470   4.001   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       6.160   5.335   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       6.160   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.850   4.001   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for HMDB0341036 (3-hydroxynona-4,6-dienoic acid)
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SMILES for HMDB0341036 (3-hydroxynona-4,6-dienoic acid)
CCC=CC=CC(O)CC(O)=O
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INCHI for HMDB0341036 (3-hydroxynona-4,6-dienoic acid)
InChI=1S/C9H14O3/c1-2-3-4-5-6-8(10)7-9(11)12/h3-6,8,10H,2,7H2,1H3,(H,11,12)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-Hydroxynona-4,6-dienoateGenerator
trans,trans-3-HYDROXYNONA-4,6-dienoateHMDB
Chemical FormulaC9H14O3
Average Molecular Weight170.208
Monoisotopic Molecular Weight170.094294311
IUPAC Name3-hydroxynona-4,6-dienoic acid
Traditional Name3-hydroxynona-4,6-dienoic acid
CAS Registry NumberNot Available
SMILES
CCC=CC=CC(O)CC(O)=O
InChI Identifier
InChI=1S/C9H14O3/c1-2-3-4-5-6-8(10)7-9(11)12/h3-6,8,10H,2,7H2,1H3,(H,11,12)
InChI KeyDXBPYWYTZPHKMA-UHFFFAOYSA-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
    • 

  • Branched fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Methyl-branched fatty acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Unsaturated fatty acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
PropertyValueSource
logP1.33ALOGPS
logP1.35ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)4.76ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity48.47 m³·mol⁻¹ChemAxon
Polarizability18.73 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Retention Times 
Not Available
Predicted Kovats Retention Indices
Not Available
Spectra
GC-MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-hydroxynona-4,6-dienoic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2022-08-08Wishart LabView Spectrum
MS/MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-4,6-dienoic acid  10V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-4,6-dienoic acid  20V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-4,6-dienoic acid  40V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-4,6-dienoic acid  10V, Negative-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-4,6-dienoic acid  20V, Negative-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-4,6-dienoic acid  40V, Negative-QTOFNot Available2022-08-10Wishart LabView Spectrum
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 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 Compound57374116  
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