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Showing NP-Card for Germacrone-13-al (NP0337682)

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Record Information
Version2.0
Created at2024-09-11 11:55:05 UTC
Updated at2024-09-11 11:55:05 UTC
NP-MRD IDNP0337682
Secondary Accession NumbersNone
Natural Product Identification
Common NameGermacrone-13-al
DescriptionGermacrone-13-al belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups. Germacrone-13-al is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Germacrone-13-al has been detected, but not quantified in, herbs and spices and turmerics. This could make germacrone-13-al a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0337682 (Germacrone-13-al)


  Mrv0541 01111301172D          

 17 17  0  0  0  0            999 V2000
   -1.5132    0.8819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2277    0.4694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2277   -0.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5132   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7987   -0.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7987    0.4694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0843    0.8819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0843   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6302   -0.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6302    0.4694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7987    1.2944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447    0.8819    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5132   -1.5931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0591   -0.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447   -1.5931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6302   -2.0056    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  2  0  0  0  0
  1  6  2  0  0  0  0
  7  6  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 10  1  0  0  0  0
  6 11  1  0  0  0  0
 10 12  2  0  0  0  0
  4 13  1  0  0  0  0
  9 14  2  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
M  END
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3D MOL for NP0337682 (Germacrone-13-al)

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3D SDF for NP0337682 (Germacrone-13-al)

  Mrv0541 01111301172D          

 17 17  0  0  0  0            999 V2000
   -1.5132    0.8819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2277    0.4694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2277   -0.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5132   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7987   -0.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7987    0.4694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0843    0.8819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0843   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6302   -0.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6302    0.4694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7987    1.2944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447    0.8819    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5132   -1.5931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0591   -0.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447   -1.5931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6302   -2.0056    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  2  0  0  0  0
  1  6  2  0  0  0  0
  7  6  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 10  1  0  0  0  0
  6 11  1  0  0  0  0
 10 12  2  0  0  0  0
  4 13  1  0  0  0  0
  9 14  2  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0337682

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(C=O)=C1\C\C=C(C)\CCC=C(C)CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H20O2/c1-11-5-4-6-12(2)9-15(17)14(8-7-11)13(3)10-16/h6-7,10H,4-5,8-9H2,1-3H3/b11-7+,12-6-,14-13+

> <INCHI_KEY>
QYFIJPMUVNMVMC-IJHCSQTGSA-N

> <FORMULA>
C15H20O2

> <MOLECULAR_WEIGHT>
232.3181

> <EXACT_MASS>
232.146329884

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
25.893702999083168

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1E,3E)-4,8-dimethyl-10-oxocyclodeca-3,7-dien-1-ylidene]propanal

> <ALOGPS_LOGP>
3.05

> <JCHEM_LOGP>
3.143728417

> <ALOGPS_LOGS>
-3.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.53562171713191

> <JCHEM_PKA_STRONGEST_BASIC>
-6.185957083337586

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
72.57379999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.38e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(1E,3E)-4,8-dimethyl-10-oxocyclodeca-3,7-dien-1-ylidene]propanal

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0337682 (Germacrone-13-al)
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PDB for NP0337682 (Germacrone-13-al)
HEADER    PROTEIN                                 11-JAN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-JAN-13         0                                  
HETATM    1  C   UNK     0      -2.825   1.646   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.158   0.876   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.158  -0.664   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.825  -1.434   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.491  -0.664   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.491   0.876   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.157   1.646   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.157  -1.434   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.176  -0.664   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.176   0.876   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.491   2.416   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.510   1.646   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.825  -2.974   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.510  -1.434   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.844  -0.664   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.510  -2.974   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.176  -3.744   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   13                                                  
CONECT    5    4    8                                                       
CONECT    6    1    7   11                                                  
CONECT    7    6   10                                                       
CONECT    8    5    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9    7   12                                                  
CONECT   11    6                                                            
CONECT   12   10                                                            
CONECT   13    4                                                            
CONECT   14    9   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

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3D PDB for NP0337682 (Germacrone-13-al)
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SMILES for NP0337682 (Germacrone-13-al)
C\C(C=O)=C1\C\C=C(C)\CCC=C(C)CC1=O
Download
INCHI for NP0337682 (Germacrone-13-al)
InChI=1S/C15H20O2/c1-11-5-4-6-12(2)9-15(17)14(8-7-11)13(3)10-16/h6-7,10H,4-5,8-9H2,1-3H3/b11-7+,12-6-,14-13+
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View in JSmol
Synonyms
ValueSource
(e,e,e)-2-(4,8-Dimethyl-10-oxo-3,7-cyclodecadien-1-ylidene)-propanalHMDB
Chemical FormulaC15H20O2
Average Mass232.3181 Da
Monoisotopic Mass232.14633 Da
IUPAC Name2-[(1E,3E)-4,8-dimethyl-10-oxocyclodeca-3,7-dien-1-ylidene]propanal
Traditional Name2-[(1E,3E)-4,8-dimethyl-10-oxocyclodeca-3,7-dien-1-ylidene]propanal
CAS Registry NumberNot Available
SMILES
C\C(C=O)=C1\C\C=C(C)\CCC=C(C)CC1=O
InChI Identifier
InChI=1S/C15H20O2/c1-11-5-4-6-12(2)9-15(17)14(8-7-11)13(3)10-16/h6-7,10H,4-5,8-9H2,1-3H3/b11-7+,12-6-,14-13+
InChI KeyQYFIJPMUVNMVMC-IJHCSQTGSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassSesquiterpenoids  
Direct ParentGermacrane sesquiterpenoids  
Alternative Parents
Substituents
  • Germacrane sesquiterpenoid
    • 

  • Enal
    • 

  • Alpha,beta-unsaturated aldehyde
    • 

  • Cyclic ketone
    • 

  • Ketone
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Aldehyde
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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
logP3.05ALOGPS
logP3.14ChemAxon
logS-3.4ALOGPS
pKa (Strongest Acidic)16.54ChemAxon
pKa (Strongest Basic)-6.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area34.14 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity72.57 m³·mol⁻¹ChemAxon
Polarizability25.89 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0036881  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB015839  
KNApSAcK IDC00011735  
Chemspider ID30777171  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14633001  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References