Hmdb loader

Showing metabocard for 3-Octenal (HMDB0302565)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 18:45:45 UTC
Update Date2021-09-23 18:45:45 UTC
HMDB IDHMDB0302565
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Octenal
Description3-octenal 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, 3-octenal is considered to be a fatty aldehyde lipid molecule. 3-octenal is practically insoluble (in water) and an extremely weak acidic compound (based on its pKa). 3-octenal can be found in coriander, which makes 3-octenal a potential biomarker for the consumption of this food product.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302565 (3-Octenal)


  Mrv0541 02241220492D          

  9  8  0  0  0  0            999 V2000
   -3.4618    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7474    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    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
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    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  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
Download

3D MOL for HMDB0302565 (3-Octenal)

HMDB0302565
     RDKit          3D
3-Octenal
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.0332   -0.7013    0.2341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1820   -0.5285   -1.0017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5001    0.8125   -1.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5790    1.0930    0.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5135    0.0640    0.1803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7959    0.4016    0.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9248   -0.5579    0.1809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8228   -0.2633    1.3273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8662    0.3477    1.2620 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8638    0.0874    1.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1209   -0.6635    0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8550   -1.7102    0.6880 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8412   -0.5952   -1.8845 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4028   -1.3060   -1.0332 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9798    0.8849   -2.0253 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3024    1.5845   -1.0807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0979    1.1035    1.0551 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1638    2.1065   -0.0482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3040   -0.9926    0.3214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9876    1.4593   -0.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5613   -0.3713   -0.7450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6619   -1.6107    0.1727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4841   -0.6443    2.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
M  END
Download

3D SDF for HMDB0302565 (3-Octenal)


  Mrv0541 02241220492D          

  9  8  0  0  0  0            999 V2000
   -3.4618    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7474    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    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
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    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  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302565

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H14O/c1-2-3-4-5-6-7-8-9/h5-6,8H,2-4,7H2,1H3/b6-5+

> <INCHI_KEY>
WDWAUVJQFVTKEW-AATRIKPKSA-N

> <FORMULA>
C8H14O

> <MOLECULAR_WEIGHT>
126.1962

> <EXACT_MASS>
126.10446507

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
15.675154386267765

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E)-oct-3-enal

> <ALOGPS_LOGP>
2.72

> <JCHEM_LOGP>
2.1794955486666665

> <ALOGPS_LOGS>
-2.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.16079969488348

> <JCHEM_PKA_STRONGEST_BASIC>
-7.036019798994456

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
40.4668

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.16e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3E)-oct-3-enal

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302565 (3-Octenal)

HMDB0302565
     RDKit          3D
3-Octenal
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.0332   -0.7013    0.2341 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1820   -0.5285   -1.0017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5001    0.8125   -1.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5790    1.0930    0.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5135    0.0640    0.1803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7959    0.4016    0.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9248   -0.5579    0.1809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8228   -0.2633    1.3273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8662    0.3477    1.2620 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8638    0.0874    1.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1209   -0.6635    0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8550   -1.7102    0.6880 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8412   -0.5952   -1.8845 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4028   -1.3060   -1.0332 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9798    0.8849   -2.0253 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3024    1.5845   -1.0807 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0979    1.1035    1.0551 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1638    2.1065   -0.0482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3040   -0.9926    0.3214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9876    1.4593   -0.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5613   -0.3713   -0.7450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6619   -1.6107    0.1727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4841   -0.6443    2.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
M  END
Download

PDB for HMDB0302565 (3-Octenal)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -6.462   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.128   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.795   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.461   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.127   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.207   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
Download

3D PDB for HMDB0302565 (3-Octenal)

COMPND    HMDB0302565
HETATM    1  C1  UNL     1       3.033  -0.701   0.234  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.182  -0.529  -1.002  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.500   0.813  -1.074  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.579   1.093   0.085  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.513   0.064   0.180  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.796   0.402   0.096  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.925  -0.558   0.181  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.823  -0.263   1.327  1.00  0.00           C  
HETATM    9  O1  UNL     1      -4.866   0.348   1.262  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.864   0.087   1.000  1.00  0.00           H  
HETATM   11  H2  UNL     1       4.121  -0.664   0.030  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.855  -1.710   0.688  1.00  0.00           H  
HETATM   13  H4  UNL     1       2.841  -0.595  -1.884  1.00  0.00           H  
HETATM   14  H5  UNL     1       1.403  -1.306  -1.033  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.980   0.885  -2.025  1.00  0.00           H  
HETATM   16  H7  UNL     1       2.302   1.584  -1.081  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.098   1.104   1.055  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.164   2.106  -0.048  1.00  0.00           H  
HETATM   19  H10 UNL     1      -0.304  -0.993   0.321  1.00  0.00           H  
HETATM   20  H11 UNL     1      -1.988   1.459  -0.041  1.00  0.00           H  
HETATM   21  H12 UNL     1      -3.561  -0.371  -0.745  1.00  0.00           H  
HETATM   22  H13 UNL     1      -2.662  -1.611   0.173  1.00  0.00           H  
HETATM   23  H14 UNL     1      -3.484  -0.644   2.300  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6    6   19
CONECT    6    7   20
CONECT    7    8   21   22
CONECT    8    9    9   23
END
Download

SMILES for HMDB0302565 (3-Octenal)

CCCC\C=C\CC=O
Download

INCHI for HMDB0302565 (3-Octenal)

InChI=1S/C8H14O/c1-2-3-4-5-6-7-8-9/h5-6,8H,2-4,7H2,1H3/b6-5+
Download
View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H14O
Average Molecular Weight126.1962
Monoisotopic Molecular Weight126.10446507
IUPAC Name(3E)-oct-3-enal
Traditional Name(3E)-oct-3-enal
CAS Registry NumberNot Available
SMILES
CCCC\C=C\CC=O
InChI Identifier
InChI=1S/C8H14O/c1-2-3-4-5-6-7-8-9/h5-6,8H,2-4,7H2,1H3/b6-5+
InChI KeyWDWAUVJQFVTKEW-AATRIKPKSA-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 effectNot Available
Disposition
Source
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
logP2.72ALOGPS
logP2.18ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)16.16ChemAxon
pKa (Strongest Basic)-7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity40.47 m³·mol⁻¹ChemAxon
Polarizability15.68 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]+131.35232859911
AllCCS[M+H-H2O]+127.12932859911
AllCCS[M+Na]+136.42532859911
AllCCS[M+NH4]+135.2932859911
AllCCS[M-H]-134.72232859911
AllCCS[M+Na-2H]-137.432859911
AllCCS[M+HCOO]-140.39832859911
DeepCCS[M+H]+132.59130932474
DeepCCS[M-H]-129.83430932474
DeepCCS[M-2H]-166.38130932474
DeepCCS[M+Na]+141.00230932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Octenal,1TMS,isomer #1CCCC/C=C/C=CO[Si](C)(C)C1284.4Semi standard non polar33892256
3-Octenal,1TMS,isomer #1CCCC/C=C/C=CO[Si](C)(C)C1235.2Standard non polar33892256
3-Octenal,1TMS,isomer #1CCCC/C=C/C=CO[Si](C)(C)C1343.2Standard polar33892256
3-Octenal,1TBDMS,isomer #1CCCC/C=C/C=CO[Si](C)(C)C(C)(C)C1516.0Semi standard non polar33892256
3-Octenal,1TBDMS,isomer #1CCCC/C=C/C=CO[Si](C)(C)C(C)(C)C1427.7Standard non polar33892256
3-Octenal,1TBDMS,isomer #1CCCC/C=C/C=CO[Si](C)(C)C(C)(C)C1519.5Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 10V, Positive-QTOFsplash10-004i-2900000000-f2dcfbe7feaad10bf4752016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 20V, Positive-QTOFsplash10-056r-9500000000-05c5407fa13038921cd72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 40V, Positive-QTOFsplash10-052f-9000000000-2ef12b8c07ae7546368a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 10V, Negative-QTOFsplash10-004i-0900000000-2775279a9479a38698662016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 20V, Negative-QTOFsplash10-004i-3900000000-41354871e33e10bca1192016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 40V, Negative-QTOFsplash10-0006-9000000000-8184b18117583dc9c06e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 10V, Positive-QTOFsplash10-0aor-9000000000-a3242f57a615951ceded2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 20V, Positive-QTOFsplash10-0aor-9000000000-bd778c44817254d9f17d2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 40V, Positive-QTOFsplash10-0aou-9000000000-cb0da29ce3704bcd00422021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 10V, Negative-QTOFsplash10-004i-0900000000-b08da4d2091aa16d3bd82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 20V, Negative-QTOFsplash10-0a4i-0900000000-ab05ac3d9413a628aed02021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Octenal 40V, Negative-QTOFsplash10-0gbc-9000000000-e78e65081c41be364b072021-10-21Wishart 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 IDFDB005182
KNApSAcK IDNot Available
Chemspider ID4446446
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5283325
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