Showing metabocard for Methyl nonanoate (MMDBc0033681)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:58:44 UTC
Update Date2024-10-06 23:55:47 UTC
Metabolite IDMMDBc0033681
Metabolite Identification
Common NameMethyl nonanoate
DescriptionMethyl nonanoate, also known as methyl pelargonate or 1-nonanecarboxylate, 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. Methyl nonanoate can be obtained from the formal condensation of methanol and nonanoic acid. It is a colourless, oily liquid with a fruity, tropical or pear-like odour, used in perfumes and flavours. It has a waxy, wine-like, green celery flavour. Methyl nonanoate is a very hydrophobic molecule, with a high boiling point of 213 oC. It is practically insoluble in water with a measured water solubility of just 22.5 mgl/L. Outside the human body, methyl nonanoate is found in a number of foods including apples, bananas, blackberries, butter, blue cheese, grapes, hop oil, pineapples, baked potatoes, star fruit, strawberries, tobacco, vanilla and white wine. Methyl nonanoate exhibits nematicidal activity against root-knot and soybean cyst nematodes and was found to be toxic to nematodes at concentrations as low as 0.2 uL a.i./litre (PMID: 19274268 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645c65dab58>

NON
  Mrv1652305271900212D          

 12 11  0  0  0  0            999 V2000
    2.8556   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1411   -1.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4266   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7121   -1.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0025   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7170   -1.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4315   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1461   -1.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8605   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8556   -0.5511    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5702   -1.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2847   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 10  2  0  0  0  0
  1 11  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  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00005645c65dab58>

HMDB0031264
     RDKit          3D
Methyl nonanoate
 32 31  0  0  0  0  0  0  0  0999 V2000
   -4.3631    0.3603   -1.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2864   -0.5247    0.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9696   -1.2122    0.2872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8102   -0.2434    0.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5748   -1.0728    0.5438 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7070   -0.2790    0.6798 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.6067   -0.5091 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2073    1.3841   -0.3556 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4317    0.5775   -0.2657 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4106   -0.6644   -0.3823 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6665    1.1676   -0.0464 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8630    0.4328    0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6177    1.3990   -0.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2116    0.0935   -1.7431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4531    0.3631   -1.6821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0526   -1.3405   -0.0078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5890    0.0047    1.0664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7797   -1.9559   -0.4966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0039   -1.7827    1.2567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7382    0.2969   -0.5670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9720    0.4646    1.2317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4785   -1.6920   -0.3732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6649   -1.7059    1.4482 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5095   -1.0326    0.7439 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7470    0.2975    1.6207 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0714    1.2603   -0.6935 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0792   -0.0009   -1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1680    1.9975    0.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3131    2.1411   -1.1831 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4462    0.5503   -0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4212    0.7611    0.9355 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5750   -0.6516    0.1457 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  1  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
  6 25  1  0
  7 26  1  0
  7 27  1  0
  8 28  1  0
  8 29  1  0
 12 30  1  0
 12 31  1  0
 12 32  1  0
M  END
Download

3D SDF for #<Metabolite:0x00005645c65dab58>

NON
  Mrv1652305271900212D          

 12 11  0  0  0  0            999 V2000
    2.8556   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1411   -1.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4266   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7121   -1.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0025   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7170   -1.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4315   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1461   -1.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8605   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8556   -0.5511    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5702   -1.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2847   -1.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 10  2  0  0  0  0
  1 11  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  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033681

> <DATABASE_NAME>
MIME

> <SMILES>
CCCCCCCCC(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C10H20O2/c1-3-4-5-6-7-8-9-10(11)12-2/h3-9H2,1-2H3

> <INCHI_KEY>
IJXHLVMUNBOGRR-UHFFFAOYSA-N

> <FORMULA>
C10H20O2

> <MOLECULAR_WEIGHT>
172.2646

> <EXACT_MASS>
172.146329884

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
21.667003750042227

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl nonanoate

> <ALOGPS_LOGP>
3.96

> <JCHEM_LOGP>
3.2904961786666655

> <ALOGPS_LOGS>
-3.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.0239806136690355

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
49.6457

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.55e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl nonanoate (ester)

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for #<Metabolite:0x00005645c65dab58>

HMDB0031264
     RDKit          3D
Methyl nonanoate
 32 31  0  0  0  0  0  0  0  0999 V2000
   -4.3631    0.3603   -1.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2864   -0.5247    0.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9696   -1.2122    0.2872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8102   -0.2434    0.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5748   -1.0728    0.5438 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7070   -0.2790    0.6798 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.6067   -0.5091 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2073    1.3841   -0.3556 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4317    0.5775   -0.2657 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4106   -0.6644   -0.3823 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6665    1.1676   -0.0464 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8630    0.4328    0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6177    1.3990   -0.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2116    0.0935   -1.7431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4531    0.3631   -1.6821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0526   -1.3405   -0.0078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5890    0.0047    1.0664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7797   -1.9559   -0.4966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0039   -1.7827    1.2567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7382    0.2969   -0.5670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9720    0.4646    1.2317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4785   -1.6920   -0.3732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6649   -1.7059    1.4482 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5095   -1.0326    0.7439 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7470    0.2975    1.6207 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0714    1.2603   -0.6935 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0792   -0.0009   -1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1680    1.9975    0.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3131    2.1411   -1.1831 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4462    0.5503   -0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4212    0.7611    0.9355 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5750   -0.6516    0.1457 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  1  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
  6 25  1  0
  7 26  1  0
  7 27  1  0
  8 28  1  0
  8 29  1  0
 12 30  1  0
 12 31  1  0
 12 32  1  0
M  END
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PDB for #<Metabolite:0x00005645c65dab58>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: NON                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       5.330  -2.569   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.997  -3.339   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.663  -2.569   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.329  -3.339   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.005  -2.569   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.338  -3.339   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.672  -2.569   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.006  -3.339   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.340  -2.569   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.330  -1.029   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.664  -3.339   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       7.998  -2.569   0.000  0.00  0.00           C+0
CONECT    1    2   10   11                                                  
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                                                            
CONECT   10    1                                                            
CONECT   11    1   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for #<Metabolite:0x00005645c65dab58>

COMPND    HMDB0031264
HETATM    1  C1  UNL     1      -4.363   0.360  -1.071  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.286  -0.525   0.142  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.970  -1.212   0.287  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.810  -0.243   0.409  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.575  -1.073   0.544  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.707  -0.279   0.680  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.948   0.607  -0.509  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.207   1.384  -0.356  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.432   0.578  -0.266  1.00  0.00           C  
HETATM   10  O1  UNL     1       3.411  -0.664  -0.382  1.00  0.00           O  
HETATM   11  O2  UNL     1       4.666   1.168  -0.046  1.00  0.00           O  
HETATM   12  C10 UNL     1       5.863   0.433   0.046  1.00  0.00           C  
HETATM   13  H1  UNL     1      -4.618   1.399  -0.707  1.00  0.00           H  
HETATM   14  H2  UNL     1      -5.212   0.094  -1.743  1.00  0.00           H  
HETATM   15  H3  UNL     1      -3.453   0.363  -1.682  1.00  0.00           H  
HETATM   16  H4  UNL     1      -5.053  -1.340  -0.008  1.00  0.00           H  
HETATM   17  H5  UNL     1      -4.589   0.005   1.066  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.780  -1.956  -0.497  1.00  0.00           H  
HETATM   19  H7  UNL     1      -3.004  -1.783   1.257  1.00  0.00           H  
HETATM   20  H8  UNL     1      -1.738   0.297  -0.567  1.00  0.00           H  
HETATM   21  H9  UNL     1      -1.972   0.465   1.232  1.00  0.00           H  
HETATM   22  H10 UNL     1      -0.478  -1.692  -0.373  1.00  0.00           H  
HETATM   23  H11 UNL     1      -0.665  -1.706   1.448  1.00  0.00           H  
HETATM   24  H12 UNL     1       1.509  -1.033   0.744  1.00  0.00           H  
HETATM   25  H13 UNL     1       0.747   0.297   1.621  1.00  0.00           H  
HETATM   26  H14 UNL     1       0.071   1.260  -0.693  1.00  0.00           H  
HETATM   27  H15 UNL     1       1.079  -0.001  -1.455  1.00  0.00           H  
HETATM   28  H16 UNL     1       2.168   1.998   0.583  1.00  0.00           H  
HETATM   29  H17 UNL     1       2.313   2.141  -1.183  1.00  0.00           H  
HETATM   30  H18 UNL     1       6.446   0.550  -0.907  1.00  0.00           H  
HETATM   31  H19 UNL     1       6.421   0.761   0.936  1.00  0.00           H  
HETATM   32  H20 UNL     1       5.575  -0.652   0.146  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   24   25
CONECT    7    8   26   27
CONECT    8    9   28   29
CONECT    9   10   10   11
CONECT   11   12
CONECT   12   30   31   32
END
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SMILES for #<Metabolite:0x00005645c65dab58>

CCCCCCCCC(=O)OC
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INCHI for #<Metabolite:0x00005645c65dab58>

InChI=1S/C10H20O2/c1-3-4-5-6-7-8-9-10(11)12-2/h3-9H2,1-2H3
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Synonyms
ValueSource
1-Nonanecarboxylic acidChEBI
Methyl ester nonanoic acidChEBI
Methyl N-nonanoateChEBI
Methyl nonylateChEBI
Methyl pelargonateChEBI
Pelargonic acid methyl esterChEBI
1-NonanecarboxylateGenerator
Methyl ester nonanoateGenerator
Methyl N-nonanoic acidGenerator
Methyl nonylic acidGenerator
Methyl pelargonic acidGenerator
Pelargonate methyl esterGenerator
Methyl nonanoic acidGenerator
FEMA 2724HMDB
Nonanoic acid methyl esterHMDB
Methyl nonanoic acid (ester)Generator, HMDB
Molecular FormulaC10H20O2
Average Mass172.2646
Monoisotopic Mass172.146329884
IUPAC Namemethyl nonanoate
Traditional Namemethyl nonanoate (ester)
CAS Registry Number1731-84-6
SMILES
CCCCCCCCC(=O)OC
InChI Identifier
InChI=1S/C10H20O2/c1-3-4-5-6-7-8-9-10(11)12-2/h3-9H2,1-2H3
InChI KeyIJXHLVMUNBOGRR-UHFFFAOYSA-N