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Showing metabocard for (Z)-3-Hexenal (HMDB0031498)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:43:41 UTC
Update Date2023-02-21 17:20:40 UTC
HMDB IDHMDB0031498
Secondary Accession Numbers
  • HMDB31498
Metabolite Identification
Common Name(Z)-3-Hexenal
Description(Z)-3-Hexenal, also known as (3Z)-hexenal, belongs to the class of organic compounds known as medium-chain aldehydes. These are an aldehyde with a chain length containing between 6 and 12 carbon atoms. Thus, (Z)-3-hexenal is considered to be a fatty aldehyde (Z)-3-Hexenal is an apple, fatty, and fruity tasting compound (Z)-3-Hexenal has been detected, but not quantified in, several different foods, such as lima beans (Phaseolus lunatus), lambsquarters (Chenopodium album), kombus (Saccharina japonica), arrowroots (Maranta arundinacea), and oregon yampahs (Perideridia oregana). This could make (Z)-3-hexenal a potential biomarker for the consumption of these foods (Z)-3-Hexenal 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 (Z)-3-Hexenal.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031498 ((Z)-3-Hexenal)

  Mrv1652309082023492D          

  7  6  0  0  0  0            999 V2000
10005.552910004.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.378310004.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.839610004.5718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10007.093110004.5718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.124210004.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10007.807610004.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.124210005.8092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  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  2  0  0  0  0
M  END
Download

3D MOL for HMDB0031498 ((Z)-3-Hexenal)

HMDB0031498
     RDKit          3D
(Z)-3-Hexenal
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.5060   -0.0939    0.5160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1695    0.6520    0.3926 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5328    0.3274   -0.9042 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6431   -0.2357   -0.9681 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5258   -0.6405    0.1234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8498    0.0576    0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1355    0.8602   -0.7880 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2668   -1.1645    0.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2098    0.2411   -0.2905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8882    0.1567    1.5303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3787    1.7587    0.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5986    0.3592    1.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0627    0.5659   -1.8447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0397   -0.4412   -1.9864 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6959   -1.7602    0.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1415   -0.4743    1.1336 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5819   -0.1686    0.8317 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
M  END
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3D SDF for HMDB0031498 ((Z)-3-Hexenal)

  Mrv1652309082023492D          

  7  6  0  0  0  0            999 V2000
10005.552910004.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.378310004.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.839610004.5718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10007.093110004.5718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.124210004.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10007.807610004.9838    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.124210005.8092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  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  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031498

> <DATABASE_NAME>
hmdb

> <SMILES>
CC\C=C/CC=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O/c1-2-3-4-5-6-7/h3-4,6H,2,5H2,1H3/b4-3-

> <INCHI_KEY>
GXANMBISFKBPEX-ARJAWSKDSA-N

> <FORMULA>
C6H10O

> <MOLECULAR_WEIGHT>
98.143

> <EXACT_MASS>
98.073164942

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.410957587491072

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3Z)-hex-3-enal

> <ALOGPS_LOGP>
1.61

> <JCHEM_LOGP>
1.2903582186666664

> <ALOGPS_LOGS>
-1.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.394264196820682

> <JCHEM_PKA_STRONGEST_BASIC>
-7.03601977213107

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
31.2648

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.44e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cis-3-hexenal

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0031498 ((Z)-3-Hexenal)

HMDB0031498
     RDKit          3D
(Z)-3-Hexenal
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.5060   -0.0939    0.5160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1695    0.6520    0.3926 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5328    0.3274   -0.9042 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6431   -0.2357   -0.9681 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5258   -0.6405    0.1234 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8498    0.0576    0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1355    0.8602   -0.7880 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2668   -1.1645    0.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2098    0.2411   -0.2905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8882    0.1567    1.5303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3787    1.7587    0.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5986    0.3592    1.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0627    0.5659   -1.8447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0397   -0.4412   -1.9864 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6959   -1.7602    0.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1415   -0.4743    1.1336 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5819   -0.1686    0.8317 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
M  END
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PDB for HMDB0031498 ((Z)-3-Hexenal)

HEADER    PROTEIN                                 08-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-20         0                                  
HETATM    1  C   UNK     0    8677.0328675.970   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8678.5738675.970   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8675.7018675.201   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8679.9078675.201   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8674.3658675.970   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8681.2418675.970   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0    8674.3658677.511   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0031498 ((Z)-3-Hexenal)

COMPND    HMDB0031498
HETATM    1  C1  UNL     1      -2.506  -0.094   0.516  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.169   0.652   0.393  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.533   0.327  -0.904  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.643  -0.236  -0.968  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.526  -0.641   0.123  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.850   0.058   0.069  1.00  0.00           C  
HETATM    7  O1  UNL     1       3.135   0.860  -0.788  1.00  0.00           O  
HETATM    8  H1  UNL     1      -2.267  -1.164   0.412  1.00  0.00           H  
HETATM    9  H2  UNL     1      -3.210   0.241  -0.290  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.888   0.157   1.530  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.379   1.759   0.430  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.599   0.359   1.279  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.063   0.566  -1.845  1.00  0.00           H  
HETATM   14  H7  UNL     1       1.040  -0.441  -1.986  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.696  -1.760   0.065  1.00  0.00           H  
HETATM   16  H9  UNL     1       1.141  -0.474   1.134  1.00  0.00           H  
HETATM   17  H10 UNL     1       3.582  -0.169   0.832  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4    4   13
CONECT    4    5   14
CONECT    5    6   15   16
CONECT    6    7    7   17
END
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SMILES for HMDB0031498 ((Z)-3-Hexenal)

CC\C=C/CC=O
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INCHI for HMDB0031498 ((Z)-3-Hexenal)

InChI=1S/C6H10O/c1-2-3-4-5-6-7/h3-4,6H,2,5H2,1H3/b4-3-
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H10O
Average Molecular Weight98.143
Monoisotopic Molecular Weight98.073164942
IUPAC Name(3Z)-hex-3-enal
Traditional Namecis-3-hexenal
CAS Registry Number6789-80-6
SMILES
CC\C=C/CC=O
InChI Identifier
InChI=1S/C6H10O/c1-2-3-4-5-6-7/h3-4,6H,2,5H2,1H3/b4-3-
InChI KeyGXANMBISFKBPEX-ARJAWSKDSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain aldehydes. These are an aldehyde with a chain length containing between 6 and 12 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentMedium-chain aldehydes
Alternative Parents
Substituents
  • Medium-chain aldehyde
  • Alpha-hydrogen aldehyde
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point20.00 °C. @ 0.20 mm HgThe Good Scents Company Information System
Water Solubility0The Good Scents Company Information System
LogP1.432 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB008085
KNApSAcK IDC00000352
Chemspider ID559032
KEGG Compound IDC16310
BioCyc IDCIS-3-HEXENAL
BiGG IDNot Available
Wikipedia LinkCis-3-Hexenal
METLIN IDNot Available
PubChem Compound643941
PDB IDNot Available
ChEBI ID23292
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1013911
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .