Np mrd loader

Showing NP-Card for 3-Hexenedioic acid (NP0000282)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:14:16 UTC
NP-MRD IDNP0000282
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000282 (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
Download

3D MOL for NP0000282 (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 NP0000282 (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>
NP0000282

> <DATABASE_NAME>
NP-MRD

> <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 NP0000282 (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

PDB for NP0000282 (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
Download

3D PDB for NP0000282 (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 NP0000282 (3-Hexenedioic acid)

OC(=O)C\C=C\CC(O)=O
Download

INCHI for NP0000282 (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 JSmol
Synonyms
ValueSource
(e)-3-Hexenedioic acidChEBI
(e)-Hex-3-enedioic acidChEBI
(e)-3-HexenedioateGenerator
(e)-Hex-3-enedioateGenerator
3-HexenedioateGenerator
trans-2-Butene-1,4-dicarboxylateHMDB
trans-2-Butene-1,4-dicarboxylic acidHMDB
trans-3-HexenedioateHMDB
trans-3-Hexenedioic acidHMDB
trans-b-HydromuconateHMDB
trans-b-Hydromuconic acidHMDB
trans-beta-HydromuconateHMDB
trans-beta-Hydromuconic acidHMDB
cis,cis-MuconateHMDB
Muconic acidHMDB
trans,trans-Muconic acidHMDB
Muconic acid, (e,e)-isomerHMDB
Chemical FormulaC6H8O4
Average Mass144.1253 Da
Monoisotopic Mass144.04226 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility17 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility10.9 g/LALOGPS
logP0.29ALOGPS
logP0.13ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)3.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity33.86 m³·mol⁻¹ChemAxon
Polarizability13.44 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000393
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDNot Available
References
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 ]
  4. Wang Y, Bi C, Pang W, Liu Y, Yuan Y, Zhao H, Zhang T, Zhao Y, Li Y: Plasma Metabolic Profiling Analysis of Gout Party on Acute Gout Arthritis Rats Based on UHPLC-Q-TOF/MS Combined with Multivariate Statistical Analysis. Int J Mol Sci. 2019 Nov 15;20(22). pii: ijms20225753. doi: 10.3390/ijms20225753. [PubMed:31731809 ]
  5. Esch P, Fischer M, Heiles S, Schafer M: Olefinic reagents tested for peptide derivatization with switchable properties: Stable upon collision induced dissociation and cleavable by in-source Paterno-Buchi reactions. J Mass Spectrom. 2019 Dec;54(12):976-986. doi: 10.1002/jms.4474. Epub 2019 Nov 28. [PubMed:31729095 ]
  6. Faccio AT, Ruperez FJ, Singh NS, Angulo S, Tavares MFM, Bernier M, Barbas C, Wainer IW: Stereochemical and structural effects of (2R,6R)-hydroxynorketamine on the mitochondrial metabolome in PC-12 cells. Biochim Biophys Acta Gen Subj. 2018 Jun;1862(6):1505-1515. doi: 10.1016/j.bbagen.2018.03.008. Epub 2018 Mar 9. [PubMed:29526507 ]
  7. Villota N, Lomas JM, Camarero LM: Effect of ultrasonic waves on the water turbidity during the oxidation of phenol. Formation of (hydro)peroxo complexes. Ultrason Sonochem. 2017 Nov;39:439-445. doi: 10.1016/j.ultsonch.2017.05.024. Epub 2017 May 16. [PubMed:28732966 ]
  8. Suastegui M, Matthiesen JE, Carraher JM, Hernandez N, Rodriguez Quiroz N, Okerlund A, Cochran EW, Shao Z, Tessonnier JP: Combining Metabolic Engineering and Electrocatalysis: Application to the Production of Polyamides from Sugar. Angew Chem Int Ed Engl. 2016 Feb 12;55(7):2368-73. doi: 10.1002/anie.201509653. Epub 2016 Jan 14. [PubMed:26840213 ]