Hmdb loader

Showing metabocard for nona-2,4,6-trienedioic acid (HMDB0341046)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2022-07-09 02:56:29 UTC
Update Date2022-07-09 02:56:29 UTC
HMDB IDHMDB0341046
Secondary Accession NumbersNone
Metabolite Identification
Common Namenona-2,4,6-trienedioic acid
Description5963-21-3 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. 5963-21-3 is a weakly acidic compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for HMDB0341046 (nona-2,4,6-trienedioic acid)


  Mrv1652304102105282D          

 13 12  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    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
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 O   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
  4  2  1  4  0  0  0
  4  5  2  0  0  0  0
  6  5  1  4  0  0  0
  6  7  2  0  0  0  0
  8  7  1  4  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
Download

3D MOL for HMDB0341046 (nona-2,4,6-trienedioic acid)

Download
3D SDF for HMDB0341046 (nona-2,4,6-trienedioic acid)

  Mrv1652304102105282D          

 13 12  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    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
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 O   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
  4  2  1  4  0  0  0
  4  5  2  0  0  0  0
  6  5  1  4  0  0  0
  6  7  2  0  0  0  0
  8  7  1  4  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341046

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H10O4/c10-8(11)6-4-2-1-3-5-7-9(12)13/h1-6H,7H2,(H,10,11)(H,12,13)

> <INCHI_KEY>
AGKRSTRNNNZIHN-UHFFFAOYSA-N

> <FORMULA>
C9H10O4

> <MOLECULAR_WEIGHT>
182.175

> <EXACT_MASS>
182.057908802

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
18.442392425345023

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
nona-2,4,6-trienedioic acid

> <ALOGPS_LOGP>
1.35

> <JCHEM_LOGP>
1.098340534

> <ALOGPS_LOGS>
-2.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.837400458543672

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.982772455942499

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
49.86850000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.39e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nona-2,4,6-trienedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0341046 (nona-2,4,6-trienedioic acid)
Download
PDB for HMDB0341046 (nona-2,4,6-trienedioic 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  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.080  -2.667   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -3.080   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Download
3D PDB for HMDB0341046 (nona-2,4,6-trienedioic acid)
Download
SMILES for HMDB0341046 (nona-2,4,6-trienedioic acid)
OC(=O)CC=CC=CC=CC(O)=O
Download
INCHI for HMDB0341046 (nona-2,4,6-trienedioic acid)
InChI=1S/C9H10O4/c10-8(11)6-4-2-1-3-5-7-9(12)13/h1-6H,7H2,(H,10,11)(H,12,13)
Download
View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC9H10O4
Average Molecular Weight182.175
Monoisotopic Molecular Weight182.057908802
IUPAC Namenona-2,4,6-trienedioic acid
Traditional Namenona-2,4,6-trienedioic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CC=CC=CC=CC(O)=O
InChI Identifier
InChI=1S/C9H10O4/c10-8(11)6-4-2-1-3-5-7-9(12)13/h1-6H,7H2,(H,10,11)(H,12,13)
InChI KeyAGKRSTRNNNZIHN-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
    • 

  • Unsaturated fatty acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • 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
logP1.35ALOGPS
logP1.1ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)3.98ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity49.87 m³·mol⁻¹ChemAxon
Polarizability18.44 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
GC-MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - nona-2,4,6-trienedioic acid GC-MS (TMS_2_1) - 70eV, PositiveNot Available2022-08-08Wishart LabView Spectrum
MS/MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nona-2,4,6-trienedioic acid  10V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nona-2,4,6-trienedioic acid  20V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nona-2,4,6-trienedioic acid  40V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nona-2,4,6-trienedioic acid  10V, Negative-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nona-2,4,6-trienedioic acid  20V, Negative-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nona-2,4,6-trienedioic 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 ID26540221  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53440988  
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