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Showing NP-Card for Methylgeraniate (NP0046810)

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Record Information
Version2.0
Created at2022-03-17 20:29:54 UTC
Updated at2022-03-17 20:29:54 UTC
NP-MRD IDNP0046810
Secondary Accession NumbersNone
Natural Product Identification
Common NameMethylgeraniate
DescriptionMethyl geranate belongs to the class of organic compounds known as acyclic monoterpenoids. These are monoterpenes that do not contain a cycle. Methyl geranate is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Methyl geranate is found, on average, in the highest concentration within lemon balms. Methyl geranate has also been detected, but not quantified in, cucumbers. This could make methyl geranate a potential biomarker for the consumption of these foods. Methylgeraniate is found in Aloysia triphylla, Aster scaber, Baccharis dracunculifolia, Bellis perennis, Carica papaya , Daphne odora, Acca sellowiana, Humulus lupulus , Leptospermum scoparium , Myrtus communis , Perilla frutescens and Zingiber mioga. These are monoterpenes (compounds made of two consecutive isoprene units) that do not contain a cycle.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0046810 (Methylgeraniate)

Geranoate (trans-methyl)
  Mrv1572001071617082D          
  Mrv0541 01091316342D          
 13 12  0  0  0  0            999 V2000
   -2.4501    1.0765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4501    0.2515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7356   -0.1610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1646   -0.1610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7356    1.4890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0212    1.0765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3067    1.4890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3067    2.3140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4078    1.0765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1222    1.4890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8367    1.0765    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5512    1.4890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1222    2.3140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  1  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
  7  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  2  0  0  0  0
M  END
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3D MOL for NP0046810 (Methylgeraniate)

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3D SDF for NP0046810 (Methylgeraniate)
Geranoate (trans-methyl)
  Mrv1572001071617082D          
  Mrv0541 01091316342D          
 13 12  0  0  0  0            999 V2000
   -2.4501    1.0765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4501    0.2515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7356   -0.1610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1646   -0.1610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7356    1.4890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0212    1.0765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3067    1.4890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3067    2.3140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4078    1.0765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1222    1.4890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8367    1.0765    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5512    1.4890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1222    2.3140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  1  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
  7  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0046810

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)\C=C(/C)CCC=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C11H18O2/c1-9(2)6-5-7-10(3)8-11(12)13-4/h6,8H,5,7H2,1-4H3/b10-8+

> <INCHI_KEY>
ACOBBFVLNKYODD-CSKARUKUSA-N

> <FORMULA>
C11H18O2

> <MOLECULAR_WEIGHT>
182.263

> <EXACT_MASS>
182.13067982

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
21.678634490321492

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (2E)-3,7-dimethylocta-2,6-dienoate

> <ALOGPS_LOGP>
3.67

> <JCHEM_LOGP>
3.2018852233333335

> <ALOGPS_LOGS>
-2.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.794097333724184

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
55.8186

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.76e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2E)-3,7-dimethylocta-2,6-dienoate

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0046810 (Methylgeraniate)
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PDB for NP0046810 (Methylgeraniate)
HEADER    PROTEIN                                 07-JAN-16   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Geranoate (trans-methyl)                          
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-JAN-16         0                                  
HETATM    1  C   UNK     0      -4.574   2.009   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.574   0.469   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.240  -0.301   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.907  -0.301   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.240   2.779   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.906   2.009   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.573   2.779   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.573   4.319   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.761   2.009   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.095   2.779   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.429   2.009   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.762   2.779   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.095   4.319   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for NP0046810 (Methylgeraniate)
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SMILES for NP0046810 (Methylgeraniate)
COC(=O)\C=C(/C)CCC=C(C)C
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INCHI for NP0046810 (Methylgeraniate)
InChI=1S/C11H18O2/c1-9(2)6-5-7-10(3)8-11(12)13-4/h6,8H,5,7H2,1-4H3/b10-8+
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View in JSmol
Synonyms
ValueSource
Methyl geranic acidGenerator
Methyl (2E)-3,7-dimethylocta-2,6-dienoic acidGenerator
Methylgeraniic acidGenerator
Chemical FormulaC11H18O2
Average Mass182.2630 Da
Monoisotopic Mass182.13068 Da
IUPAC Namemethyl (2E)-3,7-dimethylocta-2,6-dienoate
Traditional Namemethyl (2E)-3,7-dimethylocta-2,6-dienoate
CAS Registry NumberNot Available
SMILES
COC(=O)\C=C(/C)CCC=C(C)C
InChI Identifier
InChI=1S/C11H18O2/c1-9(2)6-5-7-10(3)8-11(12)13-4/h6,8H,5,7H2,1-4H3/b10-8+
InChI KeyACOBBFVLNKYODD-CSKARUKUSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Aloysia triphyllaLOTUS Database
Aster scaberLOTUS Database
Baccharis dracunculifoliaLOTUS Database
Bellis perennisLOTUS Database
Carica papaya L.Plant
Cucumis sativus L.FooDB
    • Ancheng Zhou and Roger F. McFeeters. Volatile Compounds in Cucumbers Fermented in Low-Salt Condit...
Daphne odoraLOTUS Database
Feijoa sellowianaPlant
Humulus lupulusPlant
Leptospermum scopariumPlant
Melissa officinalis L.FooDB
Myrtus communisPlant
Perilla frutescensLOTUS Database
VitisFooDB
Zingiber miogaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as acyclic monoterpenoids. These are monoterpenes that do not contain a cycle.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassMonoterpenoids  
Direct ParentAcyclic monoterpenoids  
Alternative Parents
Substituents
  • Acyclic monoterpenoid
    • 

  • Fatty acid ester
    • 

  • Fatty acyl
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Enoate 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 FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP3.67ALOGPS
logP3.2ChemAxon
logS-2.7ALOGPS
pKa (Strongest Basic)-6.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity55.82 m³·mol⁻¹ChemAxon
Polarizability21.68 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0059816  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB006016  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5365910  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References