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Showing metabocard for Hex-cis-3-en-1-al (HMDB0302416)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:37:11 UTC
Update Date2021-09-23 17:37:11 UTC
HMDB IDHMDB0302416
Secondary Accession NumbersNone
Metabolite Identification
Common NameHex-cis-3-en-1-al
DescriptionHex-cis-3-en-1-al, also known as (Z)-3-hexenal, is a member of the class of compounds known as medium-chain aldehydes. Medium-chain aldehydes are an aldehyde with a chain length containing between 6 and 12 carbon atoms. Thus, hex-cis-3-en-1-al is considered to be a fatty aldehyde lipid molecule. Hex-cis-3-en-1-al is slightly soluble (in water) and an extremely weak acidic compound (based on its pKa). Hex-cis-3-en-1-al can be found in corn, highbush blueberry, and tea, which makes hex-cis-3-en-1-al a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302416 (Hex-cis-3-en-1-al)


  Mrv1533007301516532D          

  9  8  0  0  0  0            999 V2000
    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
    1.2375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  2  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
Download

3D MOL for HMDB0302416 (Hex-cis-3-en-1-al)

HMDB0302416
     RDKit          3D
Hex-cis-3-en-1-al
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.3684    0.4616    0.1111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5689   -0.7935    0.1757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1047   -0.6000    0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4268    0.5773   -0.0919 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9157    0.7841   -0.2138 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6226   -0.5321   -0.1387 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6805   -1.1775    0.8927 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9983    1.2923    0.7228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3948    0.2196    0.5056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4508    0.8241   -0.9320 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7354   -1.3523    1.1347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9287   -1.4631   -0.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5221   -1.4774    0.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1599    1.4900   -0.1383 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3113    1.3996    0.6193 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1144    1.3139   -1.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1167   -0.9669   -1.0138 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
Download

3D SDF for HMDB0302416 (Hex-cis-3-en-1-al)


  Mrv1533007301516532D          

  9  8  0  0  0  0            999 V2000
    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
    1.2375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  2  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302416

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]\C(CC)=C(\[H])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-ONEGZZNKSA-N

> <FORMULA>
C6H10O

> <MOLECULAR_WEIGHT>
98.145

> <EXACT_MASS>
98.073164942

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.562347102683674

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E)-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>
3-hexenal, (E)-

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302416 (Hex-cis-3-en-1-al)

HMDB0302416
     RDKit          3D
Hex-cis-3-en-1-al
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.3684    0.4616    0.1111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5689   -0.7935    0.1757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1047   -0.6000    0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4268    0.5773   -0.0919 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9157    0.7841   -0.2138 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6226   -0.5321   -0.1387 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6805   -1.1775    0.8927 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9983    1.2923    0.7228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3948    0.2196    0.5056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4508    0.8241   -0.9320 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7354   -1.3523    1.1347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9287   -1.4631   -0.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5221   -1.4774    0.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1599    1.4900   -0.1383 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3113    1.3996    0.6193 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1144    1.3139   -1.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1167   -0.9669   -1.0138 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 HMDB0302416 (Hex-cis-3-en-1-al)

HEADER    PROTEIN                                 30-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-15         0                                  
HETATM    1  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.080  -2.667   0.000  0.00  0.00           O+0
HETATM    8  H   UNK     0       2.310  -1.334   0.000  0.00  0.00           H+0
HETATM    9  H   UNK     0      -0.770   1.334   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0302416 (Hex-cis-3-en-1-al)

COMPND    HMDB0302416
HETATM    1  C1  UNL     1      -2.368   0.462   0.111  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.569  -0.793   0.176  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.105  -0.600   0.057  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.427   0.577  -0.092  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.916   0.784  -0.214  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.623  -0.532  -0.139  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.680  -1.177   0.893  1.00  0.00           O  
HETATM    8  H1  UNL     1      -1.998   1.292   0.723  1.00  0.00           H  
HETATM    9  H2  UNL     1      -3.395   0.220   0.506  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.451   0.824  -0.932  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.735  -1.352   1.135  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.929  -1.463  -0.644  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.522  -1.477   0.097  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.160   1.490  -0.138  1.00  0.00           H  
HETATM   15  H8  UNL     1       2.311   1.400   0.619  1.00  0.00           H  
HETATM   16  H9  UNL     1       2.114   1.314  -1.143  1.00  0.00           H  
HETATM   17  H10 UNL     1       3.117  -0.967  -1.014  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 HMDB0302416 (Hex-cis-3-en-1-al)

[H]\C(CC)=C(\[H])CC=O
Download

INCHI for HMDB0302416 (Hex-cis-3-en-1-al)

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 Stereo Labels
Synonyms
ValueSource
(Z)-3-HexenalMeSH
3-HexenalMeSH
Chemical FormulaC6H10O
Average Molecular Weight98.145
Monoisotopic Molecular Weight98.073164942
IUPAC Name(3E)-hex-3-enal
Traditional Name3-hexenal, (E)-
CAS Registry NumberNot Available
SMILES
[H]\C(CC)=C(\[H])CC=O
InChI Identifier
InChI=1S/C6H10O/c1-2-3-4-5-6-7/h3-4,6H,2,5H2,1H3/b4-3+
InChI KeyGXANMBISFKBPEX-ONEGZZNKSA-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
Not AvailableNot 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
logP1.61ALOGPS
logP1.29ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)18.39ChemAxon
pKa (Strongest Basic)-7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity31.26 m³·mol⁻¹ChemAxon
Polarizability11.56 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+124.6132859911
AllCCS[M+H-H2O]+120.17432859911
AllCCS[M+Na]+129.94732859911
AllCCS[M+NH4]+128.75132859911
AllCCS[M-H]-129.01632859911
AllCCS[M+Na-2H]-132.80132859911
AllCCS[M+HCOO]-136.98732859911
DeepCCS[M+H]+123.96830932474
DeepCCS[M-H]-121.22430932474
DeepCCS[M-2H]-158.17530932474
DeepCCS[M+Na]+133.1330932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Hex-cis-3-en-1-al,1TMS,isomer #1CC/C=C/C=CO[Si](C)(C)C1072.8Semi standard non polar33892256
Hex-cis-3-en-1-al,1TMS,isomer #1CC/C=C/C=CO[Si](C)(C)C1046.6Standard non polar33892256
Hex-cis-3-en-1-al,1TMS,isomer #1CC/C=C/C=CO[Si](C)(C)C1176.1Standard polar33892256
Hex-cis-3-en-1-al,1TBDMS,isomer #1CC/C=C/C=CO[Si](C)(C)C(C)(C)C1314.3Semi standard non polar33892256
Hex-cis-3-en-1-al,1TBDMS,isomer #1CC/C=C/C=CO[Si](C)(C)C(C)(C)C1240.4Standard non polar33892256
Hex-cis-3-en-1-al,1TBDMS,isomer #1CC/C=C/C=CO[Si](C)(C)C(C)(C)C1369.0Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 10V, Positive-QTOFsplash10-0002-9000000000-12bdaf9a6b3bd67824572016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 20V, Positive-QTOFsplash10-000t-9000000000-e1aded4ef04348f8bb632016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 40V, Positive-QTOFsplash10-052f-9000000000-11e4baaa95b766b3739f2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 10V, Negative-QTOFsplash10-0002-9000000000-8bd3bf55e81213a76b572016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 20V, Negative-QTOFsplash10-0002-9000000000-2db5c1b677eabce1e1772016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 40V, Negative-QTOFsplash10-0006-9000000000-2ebc07e0dec1ebb59a702016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 10V, Positive-QTOFsplash10-053u-9000000000-a9240823bffb248c7f042021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 20V, Positive-QTOFsplash10-0006-9000000000-cdfcae04e8849b23a83f2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 40V, Positive-QTOFsplash10-0pec-9000000000-a7727e13755c7780ee672021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 10V, Negative-QTOFsplash10-0002-9000000000-21c5ae8d52f2e0f4cd332021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 20V, Negative-QTOFsplash10-004i-9000000000-cdcf9f489c184b5771b12021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hex-cis-3-en-1-al 40V, Negative-QTOFsplash10-014l-9000000000-86a239e2de4a786536a22021-10-21Wishart 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 IDFDB004493
KNApSAcK IDC00048948
Chemspider ID558311
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound643139
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