Hmdb loader

Showing metabocard for (Z)-3-nonenal (HMDB0303857)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 05:10:40 UTC
Update Date2021-09-24 05:10:40 UTC
HMDB IDHMDB0303857
Secondary Accession NumbersNone
Metabolite Identification
Common Name(Z)-3-nonenal
Description(Z)-non-3-enal, also known as 3-nonenal or nonenal, (3Z), 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. Based on a literature review very few articles have been published on (Z)-non-3-enal.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303857 ((Z)-3-nonenal)

  Mrv1533007131513592D          

 12 11  0  0  0  0            999 V2000
   -0.1914   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    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
    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -1.9520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099   -1.1270    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  1  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  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  2  0  0  0  0
 11  6  1  0  0  0  0
 12  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0303857 ((Z)-3-nonenal)

HMDB0303857
     RDKit          3D
(Z)-3-nonenal
 26 25  0  0  0  0  0  0  0  0999 V2000
   -4.0081   -0.8162    1.0377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0432    0.2460    0.5570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7462   -0.3903    0.0941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7822    0.6742   -0.3864 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4775   -0.0376   -0.8277 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5127    0.8472   -1.3209 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6997    0.9169   -0.7533 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1596    0.1494    0.4207 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3301   -0.6914    0.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8228   -1.3807    0.9523 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6193   -1.8101    0.6768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0605   -0.8711    2.1420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9982   -0.6961    0.5595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4694    0.8289   -0.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8404    0.9742    1.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9051   -1.1964   -0.6157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2597   -0.8479    1.0033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5605    1.3297    0.4830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2319    1.2939   -1.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7782   -0.6955   -0.0113 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1853   -0.7319   -1.6744 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3501    1.4980   -2.1907 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4764    1.6114   -1.1611 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4192   -0.4119    0.9702 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5572    0.9141    1.1650 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7559   -0.7068   -0.8936 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  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  8 24  1  0
  8 25  1  0
  9 26  1  0
M  END
Download

3D SDF for HMDB0303857 ((Z)-3-nonenal)

  Mrv1533007131513592D          

 12 11  0  0  0  0            999 V2000
   -0.1914   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    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
    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -1.9520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099   -1.1270    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  1  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  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  2  0  0  0  0
 11  6  1  0  0  0  0
 12  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0303857

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]\C(CCCCC)=C(/[H])CC=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H16O/c1-2-3-4-5-6-7-8-9-10/h6-7,9H,2-5,8H2,1H3/b7-6-

> <INCHI_KEY>
YXEAENVLZOODMT-SREVYHEPSA-N

> <FORMULA>
C9H16O

> <MOLECULAR_WEIGHT>
140.226

> <EXACT_MASS>
140.120115135

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.43309618401827

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
3.35

> <JCHEM_LOGP>
2.6240642136666663

> <ALOGPS_LOGS>
-3.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.390797642325552

> <JCHEM_PKA_STRONGEST_BASIC>
-7.0360197989945865

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
45.0678

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3Z)-non-3-enal

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0303857 ((Z)-3-nonenal)

HMDB0303857
     RDKit          3D
(Z)-3-nonenal
 26 25  0  0  0  0  0  0  0  0999 V2000
   -4.0081   -0.8162    1.0377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0432    0.2460    0.5570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7462   -0.3903    0.0941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7822    0.6742   -0.3864 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4775   -0.0376   -0.8277 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5127    0.8472   -1.3209 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6997    0.9169   -0.7533 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1596    0.1494    0.4207 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3301   -0.6914    0.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8228   -1.3807    0.9523 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6193   -1.8101    0.6768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0605   -0.8711    2.1420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9982   -0.6961    0.5595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4694    0.8289   -0.3017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8404    0.9742    1.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9051   -1.1964   -0.6157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2597   -0.8479    1.0033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5605    1.3297    0.4830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2319    1.2939   -1.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7782   -0.6955   -0.0113 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1853   -0.7319   -1.6744 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3501    1.4980   -2.1907 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4764    1.6114   -1.1611 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4192   -0.4119    0.9702 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5572    0.9141    1.1650 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7559   -0.7068   -0.8936 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  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  8 24  1  0
  8 25  1  0
  9 26  1  0
M  END
Download

PDB for HMDB0303857 ((Z)-3-nonenal)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0      -0.357  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976  -2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644  -2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.977  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.311  -2.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.645  -1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.645   0.206   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.978   0.976   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.978   2.516   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       6.311  -3.644   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       8.978  -2.104   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    6                                                            
CONECT   12    7                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
Download

3D PDB for HMDB0303857 ((Z)-3-nonenal)

COMPND    HMDB0303857
HETATM    1  C1  UNL     1      -4.008  -0.816   1.038  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.043   0.246   0.557  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.746  -0.390   0.094  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.782   0.674  -0.386  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.477  -0.038  -0.828  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.513   0.847  -1.321  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.700   0.917  -0.753  1.00  0.00           C  
HETATM    8  C8  UNL     1       3.160   0.149   0.421  1.00  0.00           C  
HETATM    9  C9  UNL     1       4.330  -0.691   0.092  1.00  0.00           C  
HETATM   10  O1  UNL     1       4.823  -1.381   0.952  1.00  0.00           O  
HETATM   11  H1  UNL     1      -3.619  -1.810   0.677  1.00  0.00           H  
HETATM   12  H2  UNL     1      -4.061  -0.871   2.142  1.00  0.00           H  
HETATM   13  H3  UNL     1      -4.998  -0.696   0.559  1.00  0.00           H  
HETATM   14  H4  UNL     1      -3.469   0.829  -0.302  1.00  0.00           H  
HETATM   15  H5  UNL     1      -2.840   0.974   1.352  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.905  -1.196  -0.616  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.260  -0.848   1.003  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.561   1.330   0.483  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.232   1.294  -1.175  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.778  -0.695  -0.011  1.00  0.00           H  
HETATM   21  H11 UNL     1       0.185  -0.732  -1.674  1.00  0.00           H  
HETATM   22  H12 UNL     1       1.350   1.498  -2.191  1.00  0.00           H  
HETATM   23  H13 UNL     1       3.476   1.611  -1.161  1.00  0.00           H  
HETATM   24  H14 UNL     1       2.419  -0.412   0.970  1.00  0.00           H  
HETATM   25  H15 UNL     1       3.557   0.914   1.165  1.00  0.00           H  
HETATM   26  H16 UNL     1       4.756  -0.707  -0.894  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3   14   15
CONECT    3    4   16   17
CONECT    4    5   18   19
CONECT    5    6   20   21
CONECT    6    7    7   22
CONECT    7    8   23
CONECT    8    9   24   25
CONECT    9   10   10   26
END
Download

SMILES for HMDB0303857 ((Z)-3-nonenal)

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

INCHI for HMDB0303857 ((Z)-3-nonenal)

InChI=1S/C9H16O/c1-2-3-4-5-6-7-8-9-10/h6-7,9H,2-5,8H2,1H3/b7-6-
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
3-NonenalMeSH
Nonenal, (3Z)MeSH
8-NonenalMeSH
Chemical FormulaC9H16O
Average Molecular Weight140.226
Monoisotopic Molecular Weight140.120115135
IUPAC Name(3Z)-non-3-enal
Traditional Name(3Z)-non-3-enal
CAS Registry NumberNot Available
SMILES
[H]\C(CCCCC)=C(/[H])CC=O
InChI Identifier
InChI=1S/C9H16O/c1-2-3-4-5-6-7-8-9-10/h6-7,9H,2-5,8H2,1H3/b7-6-
InChI KeyYXEAENVLZOODMT-SREVYHEPSA-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
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
Predicted Chromatographic Properties
Spectra
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 IDFDB029674
KNApSAcK IDNot Available
Chemspider ID4936380
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6431042
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