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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:33:05 UTC

Update Date

2023-02-21 17:19:19 UTC

HMDB ID

HMDB0029859

Secondary Accession Numbers

HMDB29859

Metabolite Identification

Common Name

Methyl (xi)-3-nonenoate

Description

Methyl (xi)-3-nonenoate belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group. Based on a literature review a small amount of articles have been published on Methyl (xi)-3-nonenoate.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0029859
     RDKit          3D
Methyl (xi)-3-nonenoate
 30 29  0  0  0  0  0  0  0  0999 V2000
   -3.8043    0.5938    1.8646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2253    0.1009    0.5720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7854   -0.3355    0.8106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2272   -0.8321   -0.5269 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2372   -1.2748   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7358   -1.7389   -1.5623 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7265   -1.2963   -2.2483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6376   -0.2233   -1.9723 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5719    0.5991   -0.7947 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8693    1.6570   -0.8067 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2366    0.3236    0.3893 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1510    1.1607    1.5324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4776    1.4285    1.6782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2737   -0.2631    2.3986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9669    0.9570    2.4991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8136   -0.7353    0.1411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2113    0.9659   -0.1294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1592    0.5189    1.1232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7227   -1.1651    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2551    0.0350   -1.2167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8306   -1.6876   -0.8948 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1037   -2.1569    0.4466 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6958   -0.4480    0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1618   -2.6116   -2.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9474   -1.8213   -3.2505 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7046   -0.6650   -2.0246 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6816    0.4446   -2.9194 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0654    1.8008    1.6298 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9295    0.6101    2.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972    1.8473    1.3490 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
  9 11  1  0
 11 12  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  2 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 12 28  1  0
 12 29  1  0
 12 30  1  0
M  END

HMDB0029859
     RDKit          3D
Methyl (xi)-3-nonenoate
 30 29  0  0  0  0  0  0  0  0999 V2000
   -3.8043    0.5938    1.8646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2253    0.1009    0.5720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7854   -0.3355    0.8106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2272   -0.8321   -0.5269 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2372   -1.2748   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7358   -1.7389   -1.5623 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7265   -1.2963   -2.2483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6376   -0.2233   -1.9723 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5719    0.5991   -0.7947 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8693    1.6570   -0.8067 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2366    0.3236    0.3893 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1510    1.1607    1.5324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4776    1.4285    1.6782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2737   -0.2631    2.3986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9669    0.9570    2.4991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8136   -0.7353    0.1411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2113    0.9659   -0.1294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1592    0.5189    1.1232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7227   -1.1651    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2551    0.0350   -1.2167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8306   -1.6876   -0.8948 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1037   -2.1569    0.4466 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6958   -0.4480    0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1618   -2.6116   -2.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9474   -1.8213   -3.2505 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7046   -0.6650   -2.0246 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6816    0.4446   -2.9194 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0654    1.8008    1.6298 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9295    0.6101    2.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972    1.8473    1.3490 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
  9 11  1  0
 11 12  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  2 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 12 28  1  0
 12 29  1  0
 12 30  1  0
M  END

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -0.357  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.645   3.286   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.976  -2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644  -2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.977  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.311  -2.104   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.645  -1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.645   0.206   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.311   0.976   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.977   0.206   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.311   2.516   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2   12                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12    2   10                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

COMPND    HMDB0029859
HETATM    1  C1  UNL     1      -3.804   0.594   1.865  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.225   0.101   0.572  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.785  -0.335   0.811  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.227  -0.832  -0.527  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.237  -1.275  -0.280  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.736  -1.739  -1.562  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.727  -1.296  -2.248  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.638  -0.223  -1.972  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.572   0.599  -0.795  1.00  0.00           C  
HETATM   10  O1  UNL     1       1.869   1.657  -0.807  1.00  0.00           O  
HETATM   11  O2  UNL     1       3.237   0.324   0.389  1.00  0.00           O  
HETATM   12  C10 UNL     1       3.151   1.161   1.532  1.00  0.00           C  
HETATM   13  H1  UNL     1      -4.478   1.428   1.678  1.00  0.00           H  
HETATM   14  H2  UNL     1      -4.274  -0.263   2.399  1.00  0.00           H  
HETATM   15  H3  UNL     1      -2.967   0.957   2.499  1.00  0.00           H  
HETATM   16  H4  UNL     1      -3.814  -0.735   0.141  1.00  0.00           H  
HETATM   17  H5  UNL     1      -3.211   0.966  -0.129  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.159   0.519   1.123  1.00  0.00           H  
HETATM   19  H7  UNL     1      -1.723  -1.165   1.523  1.00  0.00           H  
HETATM   20  H8  UNL     1      -1.255   0.035  -1.217  1.00  0.00           H  
HETATM   21  H9  UNL     1      -1.831  -1.688  -0.895  1.00  0.00           H  
HETATM   22  H10 UNL     1       0.104  -2.157   0.447  1.00  0.00           H  
HETATM   23  H11 UNL     1       0.696  -0.448   0.220  1.00  0.00           H  
HETATM   24  H12 UNL     1       0.162  -2.612  -2.006  1.00  0.00           H  
HETATM   25  H13 UNL     1       1.947  -1.821  -3.251  1.00  0.00           H  
HETATM   26  H14 UNL     1       3.705  -0.665  -2.025  1.00  0.00           H  
HETATM   27  H15 UNL     1       2.682   0.445  -2.919  1.00  0.00           H  
HETATM   28  H16 UNL     1       4.065   1.801   1.630  1.00  0.00           H  
HETATM   29  H17 UNL     1       2.930   0.610   2.454  1.00  0.00           H  
HETATM   30  H18 UNL     1       2.297   1.847   1.349  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   16   17
CONECT    3    4   18   19
CONECT    4    5   20   21
CONECT    5    6   22   23
CONECT    6    7    7   24
CONECT    7    8   25
CONECT    8    9   26   27
CONECT    9   10   10   11
CONECT   11   12
CONECT   12   28   29   30
END

HMDB0029859
     RDKit          3D
Methyl (xi)-3-nonenoate
 30 29  0  0  0  0  0  0  0  0999 V2000
   -3.8043    0.5938    1.8646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2253    0.1009    0.5720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7854   -0.3355    0.8106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2272   -0.8321   -0.5269 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2372   -1.2748   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7358   -1.7389   -1.5623 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7265   -1.2963   -2.2483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6376   -0.2233   -1.9723 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5719    0.5991   -0.7947 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8693    1.6570   -0.8067 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2366    0.3236    0.3893 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1510    1.1607    1.5324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4776    1.4285    1.6782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2737   -0.2631    2.3986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9669    0.9570    2.4991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8136   -0.7353    0.1411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2113    0.9659   -0.1294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1592    0.5189    1.1232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7227   -1.1651    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2551    0.0350   -1.2167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8306   -1.6876   -0.8948 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1037   -2.1569    0.4466 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6958   -0.4480    0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1618   -2.6116   -2.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9474   -1.8213   -3.2505 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7046   -0.6650   -2.0246 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6816    0.4446   -2.9194 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0654    1.8008    1.6298 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9295    0.6101    2.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972    1.8473    1.3490 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
  9 11  1  0
 11 12  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  2 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 12 28  1  0
 12 29  1  0
 12 30  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Methyl (XI)-3-nonenoic acid	Generator
3-Nonenoic acid, methyl ester	HMDB
FEMA 3710	HMDB
Methyl 3-nonenoate	HMDB
Methyl non-3-enoate	HMDB
Methyl (3Z)-non-3-enoic acid	Generator

Chemical Formula

C₁₀H₁₈O₂

Average Molecular Weight

170.2487

Monoisotopic Molecular Weight

170.13067982

IUPAC Name

methyl (3Z)-non-3-enoate

Traditional Name

methyl (3Z)-non-3-enoate

CAS Registry Number

13481-87-3

SMILES

CCCCC\C=C/CC(=O)OC

InChI Identifier

InChI=1S/C10H18O2/c1-3-4-5-6-7-8-9-10(11)12-2/h7-8H,3-6,9H2,1-2H3/b8-7-

InChI Key

MTDCXFZGUVZRSQ-FPLPWBNLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acid esters

Direct Parent

Fatty acid methyl esters

Alternative Parents

Substituents

Fatty acid methyl ester
Methyl ester
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Cellular substructure

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0029859)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029859)

Source

Endogenous

Endogenous (HMDB: HMDB0029859)

Plant

Plant (HMDB: HMDB0029859)

Animal

Animal (HMDB: HMDB0029859)

Exogenous

Food

Food (HMDB: HMDB0029859)

Fruit

Fruits (FooDB: FOOD00871)

Exogenous (HMDB: HMDB0029859)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0029859)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0029859)

Lipid metabolism pathway (HMDB: HMDB0029859)

Cellular process

Cell signaling (HMDB: HMDB0029859)

Biochemical process

Lipid transport (HMDB: HMDB0029859)

Role

Biological role

Energy source (HMDB: HMDB0029859)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0029859)

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0029859)

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	90.00 °C. @ 18.00 mm Hg	The Good Scents Company Information System
Water Solubility	52.1 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	3.385 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.081 g/L	ALOGPS
logP	3.9	ALOGPS
logP	2.93	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Basic)	-7.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	26.3 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	50.76 m³·mol⁻¹	ChemAxon
Polarizability	20.57 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	144.168	31661259
DarkChem	[M-H]-	142.074	31661259
DeepCCS	[M+H]+	133.749	30932474
DeepCCS	[M-H]-	129.9	30932474
DeepCCS	[M-2H]-	167.009	30932474
DeepCCS	[M+Na]+	142.68	30932474
AllCCS	[M+H]+	143.6	32859911
AllCCS	[M+H-H2O]+	139.7	32859911
AllCCS	[M+NH4]+	147.2	32859911
AllCCS	[M+Na]+	148.3	32859911
AllCCS	[M-H]-	144.8	32859911
AllCCS	[M+Na-2H]-	146.5	32859911
AllCCS	[M+HCOO]-	148.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	7.85 minutes	32390414
Predicted by Siyang on May 30, 2022	17.1411 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.03 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2425.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	528.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	211.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	366.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	346.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	701.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	684.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	104.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1558.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	516.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1433.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	484.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	415.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	556.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	529.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	10.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Methyl (xi)-3-nonenoate	CCCCC\C=C/CC(=O)OC	1515.4	Standard polar	33892256
Methyl (xi)-3-nonenoate	CCCCC\C=C/CC(=O)OC	1188.3	Standard non polar	33892256
Methyl (xi)-3-nonenoate	CCCCC\C=C/CC(=O)OC	1263.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Methyl (xi)-3-nonenoate GC-MS (Non-derivatized) - 70eV, Positive	splash10-08i3-9400000000-f8dcf777756d66aacee1	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methyl (xi)-3-nonenoate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 10V, Positive-QTOF	splash10-00dr-0900000000-316151fe58be2348f1f1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 20V, Positive-QTOF	splash10-00ds-9700000000-7d3e697adbea93badd5c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 40V, Positive-QTOF	splash10-052f-9000000000-31ecaa371cd553d15e88	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 10V, Negative-QTOF	splash10-014i-0900000000-f8be32d8815670086930	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 20V, Negative-QTOF	splash10-014r-1900000000-1b6de3bc81e4e8731eb6	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 40V, Negative-QTOF	splash10-0006-9400000000-e2582a3d84b3e5afd2b8	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 10V, Positive-QTOF	splash10-067m-9200000000-bfc13f8faf34c6880e3e	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 20V, Positive-QTOF	splash10-066u-9000000000-cab0881420f337f712c6	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 40V, Positive-QTOF	splash10-0aou-9000000000-16a39c158c790b0334f9	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 10V, Negative-QTOF	splash10-00kr-0900000000-c593c483f0ad931a8aa0	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 20V, Negative-QTOF	splash10-014i-0900000000-b70501e7491b54e1afd1	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methyl (xi)-3-nonenoate 40V, Negative-QTOF	splash10-0apm-9000000000-25c653ba10be534a3e0f	2021-09-24	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001081

KNApSAcK ID

Not Available

Chemspider ID

21587164

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14690973

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1037561

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for Methyl (xi)-3-nonenoate (HMDB0029859)

MOL for HMDB0029859 (Methyl (xi)-3-nonenoate)

3D MOL for HMDB0029859 (Methyl (xi)-3-nonenoate)

3D SDF for HMDB0029859 (Methyl (xi)-3-nonenoate)

3D-SDF for HMDB0029859 (Methyl (xi)-3-nonenoate)

PDB for HMDB0029859 (Methyl (xi)-3-nonenoate)

3D PDB for HMDB0029859 (Methyl (xi)-3-nonenoate)

SMILES for HMDB0029859 (Methyl (xi)-3-nonenoate)

INCHI for HMDB0029859 (Methyl (xi)-3-nonenoate)

Structure for HMDB0029859 (Methyl (xi)-3-nonenoate)

3D Structure for HMDB0029859 (Methyl (xi)-3-nonenoate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra