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Showing metabocard for 3-Hexenedioic acid (HMDB0000393)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:46 UTC
HMDB IDHMDB0000393
Secondary Accession Numbers
  • HMDB00393
Metabolite Identification
Common Name3-Hexenedioic acid
Description3-Hexenedioic acid is a normal human unsaturated dicarboxylic acid metabolite with increased excretion in patients with Dicarboxylic aciduria caused by fatty acid metabolism disorders. (PMID 2614263 , 7096501 ) The urinary excretion of 3-Hexenedioic acid is increased in conditions of augmented mobilization of fatty acids or inhibited fatty acid oxidation. (PMID 2001377 ).
Structure
Data?1676999686
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000393 (3-Hexenedioic acid)

HMDB00393.mol
  Mrv1652305261923572D          

 10  9  0  0  0  0            999 V2000
   -2.3621    0.8465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7787    0.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818    0.4766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -0.1068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3984    0.1068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9818   -0.4766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7787   -0.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3621   -0.8465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9922   -0.5338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9922    0.5338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  9  2  0  0  0  0
  7 10  2  0  0  0  0
M  END
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3D MOL for HMDB0000393 (3-Hexenedioic acid)

HMDB0000393
     RDKit          3D
3-Hexenedioic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.5749   -0.1718    1.9544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7706   -0.1907    0.7149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8355   -0.9354    0.2362 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8757    0.5654   -0.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587   -0.0934   -0.3724 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6088    0.4447   -0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9174   -0.2195   -0.2673 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6550   -0.4217    0.9914 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3234   -1.3412    1.7817 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7275    0.3798    1.3512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2943   -0.7349   -0.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3518    0.6295   -1.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7295    1.6247    0.1751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5489   -1.0768   -0.8246 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6113    1.4196    0.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5095    0.4706   -0.9304 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8338   -1.1646   -0.8323 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3533    0.8160    0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
 10 18  1  0
M  END
Download

3D SDF for HMDB0000393 (3-Hexenedioic acid)

HMDB00393.mol
  Mrv1652305261923572D          

 10  9  0  0  0  0            999 V2000
   -2.3621    0.8465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7787    0.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818    0.4766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -0.1068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3984    0.1068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9818   -0.4766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7787   -0.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3621   -0.8465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9922   -0.5338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9922    0.5338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  2  9  2  0  0  0  0
  7 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000393

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O4/c7-5(8)3-1-2-4-6(9)10/h1-2H,3-4H2,(H,7,8)(H,9,10)/b2-1+

> <INCHI_KEY>
YHGNXQAFNHCBTK-OWOJBTEDSA-N

> <FORMULA>
C6H8O4

> <MOLECULAR_WEIGHT>
144.1253

> <EXACT_MASS>
144.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.439568169189208

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E)-hex-3-enedioic acid

> <ALOGPS_LOGP>
0.29

> <JCHEM_LOGP>
0.12873270600000009

> <ALOGPS_LOGS>
-1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.555552302893718

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.774002953571271

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
33.8556

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.09e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hexenedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000393 (3-Hexenedioic acid)

HMDB0000393
     RDKit          3D
3-Hexenedioic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.5749   -0.1718    1.9544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7706   -0.1907    0.7149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8355   -0.9354    0.2362 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8757    0.5654   -0.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587   -0.0934   -0.3724 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6088    0.4447   -0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9174   -0.2195   -0.2673 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6550   -0.4217    0.9914 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3234   -1.3412    1.7817 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7275    0.3798    1.3512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2943   -0.7349   -0.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3518    0.6295   -1.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7295    1.6247    0.1751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5489   -1.0768   -0.8246 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6113    1.4196    0.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5095    0.4706   -0.9304 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8338   -1.1646   -0.8323 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3533    0.8160    0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
 10 18  1  0
M  END
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PDB for HMDB0000393 (3-Hexenedioic acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: HMDB00393.mol                                     
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  O   UNK     0      -4.409   1.580   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -3.320   0.491   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.833   0.890   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.744  -0.199   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.744   0.199   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.833  -0.890   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.320  -0.491   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.409  -1.580   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -3.719  -0.996   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.719   0.996   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7                                                            
CONECT    9    2                                                            
CONECT   10    7                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0000393 (3-Hexenedioic acid)

COMPND    HMDB0000393
HETATM    1  O1  UNL     1      -2.575  -0.172   1.954  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.771  -0.191   0.715  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.836  -0.935   0.236  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.876   0.565  -0.156  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.559  -0.093  -0.372  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.609   0.445  -0.048  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.917  -0.220  -0.267  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.655  -0.422   0.991  1.00  0.00           C  
HETATM    9  O3  UNL     1       2.323  -1.341   1.782  1.00  0.00           O  
HETATM   10  O4  UNL     1       3.728   0.380   1.351  1.00  0.00           O  
HETATM   11  H1  UNL     1      -4.294  -0.735  -0.645  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.352   0.629  -1.176  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.730   1.625   0.175  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.549  -1.077  -0.825  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.611   1.420   0.402  1.00  0.00           H  
HETATM   16  H6  UNL     1       2.510   0.471  -0.930  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.834  -1.165  -0.832  1.00  0.00           H  
HETATM   18  H8  UNL     1       4.353   0.816   0.703  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   12   13
CONECT    5    6    6   14
CONECT    6    7   15
CONECT    7    8   16   17
CONECT    8    9    9   10
CONECT   10   18
END
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SMILES for HMDB0000393 (3-Hexenedioic acid)

OC(=O)C\C=C\CC(O)=O
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INCHI for HMDB0000393 (3-Hexenedioic acid)

InChI=1S/C6H8O4/c7-5(8)3-1-2-4-6(9)10/h1-2H,3-4H2,(H,7,8)(H,9,10)/b2-1+
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H8O4
Average Molecular Weight144.1253
Monoisotopic Molecular Weight144.042258744
IUPAC Name(3E)-hex-3-enedioic acid
Traditional Name3-hexenedioic acid
CAS Registry Number29311-53-3
SMILES
OC(=O)C\C=C\CC(O)=O
InChI Identifier
InChI=1S/C6H8O4/c7-5(8)3-1-2-4-6(9)10/h1-2H,3-4H2,(H,7,8)(H,9,10)/b2-1+
InChI KeyYHGNXQAFNHCBTK-OWOJBTEDSA-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 Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility17 mg/mLNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022011
KNApSAcK IDNot Available
Chemspider ID4508880
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5382
PubChem Compound5351896
PDB IDNot Available
ChEBI ID86952
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceStille, J. K. Carbonylation of diolefins. Belg. (1979), 19 pp. CODEN: BEXXAL BE 877770 19791116 CAN 92:214907 AN 1980:214907
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Tserng KY, Jin SJ: Metabolic origin of urinary 3-hydroxy dicarboxylic acids. Biochemistry. 1991 Mar 5;30(9):2508-14. [PubMed:2001377 ]
  2. Jin SJ, Tserng KY: Identification of isomeric unsaturated medium-chain dicarboxylic acids in human urine. J Lipid Res. 1989 Oct;30(10):1611-9. [PubMed:2614263 ]
  3. Tanaka K, Hine DG: Compilation of gas chromatographic retention indices of 163 metabolically important organic acids, and their use in detection of patients with organic acidurias. J Chromatogr. 1982 Apr 30;239:301-22. [PubMed:7096501 ]