NP-MRD: Showing NP-Card for Germacra-1(10),4,11(13)-trien-12-oic acid (NP0075367)

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Record Information

Version

2.0

Created at

2022-04-28 20:38:58 UTC

Updated at

2022-04-28 20:38:59 UTC

NP-MRD ID

NP0075367

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Germacra-1(10),4,11(13)-trien-12-oic acid

Description

Germacra-1(10),4,11(13)-trien-12-oic acid, also known as germacrene acid, 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. Germacra-1(10),4,11(13)-trien-12-oic acid is found in Artemisia annua , Barnadesia spinosa, Hilianthus annuus and Saussurea iappa. Germacra-1(10),4,11(13)-trien-12-oic acid was first documented in 2002 (PMID: 12011356). Based on a literature review very few articles have been published on germacra-1(10),4,11(13)-trien-12-oic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 39  0  0  0  0  0  0  0  0999 V2000
    2.8452   -1.9339   -0.3901 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6628   -1.1831    0.6768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8095   -0.7136    1.4179 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9600   -1.0172    1.0452 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6419    0.0686    2.5357 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2586   -0.8565    1.0784 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0141    0.6474    1.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6277    1.1145   -0.2948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4452    1.8313   -0.5912 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7133    2.2365   -2.0133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4542    2.2853    0.4283 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6352    1.3918    0.4057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6558    0.3745   -0.6513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0086   -0.7833   -0.6233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0790   -1.7736   -1.7441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1508   -1.1852    0.5487 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2621   -1.5134    0.1444 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8635   -2.1691   -0.6788 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0591   -2.3400   -1.0120 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1282   -0.1318    3.4026 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1001   -1.2562    2.0928 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2819    0.8796    1.8414 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9649    1.1247    1.3688 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3179    0.8209   -1.1041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2708    3.2652   -2.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1838    1.6044   -2.7287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7731    2.3342   -2.2372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7650    3.3012    0.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9871    2.4145    1.4213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5431    2.0222    0.3295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7214    0.9447    1.4386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2480    0.5755   -1.5385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7961   -2.7773   -1.4477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0964   -1.8231   -2.1804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3340   -1.4236   -2.5079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2072   -0.4160    1.3557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5550   -2.1141    1.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4447   -2.6244    0.1559 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3808   -1.2013   -0.9068 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  2  0
  8  7  1  0
  7  6  1  0
  6 17  1  0
 17 16  1  0
 16 14  1  0
 14 15  1  0
 14 13  2  0
 13 12  1  0
 12 11  1  0
  6  2  1  0
  2  1  2  3
  2  3  1  0
  3  5  1  0
  3  4  2  0
 11  9  1  0
 10 25  1  0
 10 26  1  0
 10 27  1  0
  8 24  1  0
  7 22  1  0
  7 23  1  0
  6 21  1  1
 17 38  1  0
 17 39  1  0
 16 36  1  0
 16 37  1  0
 15 33  1  0
 15 34  1  0
 15 35  1  0
 13 32  1  0
 12 30  1  0
 12 31  1  0
 11 28  1  0
 11 29  1  0
  1 18  1  0
  1 19  1  0
  5 20  1  0
M  END


  Mrv1652304282222382D          

 17 17  0  0  1  0            999 V2000
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9139    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   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  2  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
  9 10  2  0  0  0  0
  1 10  1  0  0  0  0
  9 11  1  0  0  0  0
  6 12  1  6  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  3 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0075367

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C1=C/C[C@@H](CC\C(C)=C\CC1)C(=C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O2/c1-11-5-4-6-12(2)8-10-14(9-7-11)13(3)15(16)17/h5,8,14H,3-4,6-7,9-10H2,1-2H3,(H,16,17)/b11-5+,12-8+/t14-/m1/s1

> <INCHI_KEY>
IBJVPIJUFFVDBS-JBMXZMKISA-N

> <FORMULA>
C15H22O2

> <MOLECULAR_WEIGHT>
234.339

> <EXACT_MASS>
234.161979948

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.271275074439465

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1R,3E,7E)-4,8-dimethylcyclodeca-3,7-dien-1-yl]prop-2-enoic acid

> <ALOGPS_LOGP>
4.17

> <JCHEM_LOGP>
4.071219525666668

> <ALOGPS_LOGS>
-3.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.147416103317341

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
72.0001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.31e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
germacrene acid

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.573   0.294   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9    1                                                       
CONECT   11    9                                                            
CONECT   12    6   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    3                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Value	Source
Germacrene acid	ChEBI
Germacra-1(10),4,11(13)-trien-12-Oate	Kegg

Chemical Formula

C₁₅H₂₂O₂

Average Mass

234.3390 Da

Monoisotopic Mass

234.16198 Da

IUPAC Name

2-[(1R,3E,7E)-4,8-dimethylcyclodeca-3,7-dien-1-yl]prop-2-enoic acid

Traditional Name

germacrene acid

CAS Registry Number

Not Available

SMILES

C\C1=C/C[C@@H](CC\C(C)=C\CC1)C(=C)C(O)=O

InChI Identifier

InChI=1S/C15H22O2/c1-11-5-4-6-12(2)8-10-14(9-7-11)13(3)15(16)17/h5,8,14H,3-4,6-7,9-10H2,1-2H3,(H,16,17)/b11-5+,12-8+/t14-/m1/s1

InChI Key

IBJVPIJUFFVDBS-JBMXZMKISA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Artemisia annua	Plant	KNApSAcK
Barnadesia spinosa	Plant	KNApSAcK
Hilianthus annuus	-	KNApSAcK
Saussurea iappa	Plant	KNApSAcK

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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Germacrane sesquiterpenoids

Alternative Parents

Substituents

Germacrane sesquiterpenoid
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

monocarboxylic acid (CHEBI:61305 )
germacrane sesquiterpenoid (CHEBI:61305 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	4.17	ALOGPS
logP	4.07	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	5.15	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	72 m³·mol⁻¹	ChemAxon
Polarizability	26.27 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25245825

PDB ID

Not Available

ChEBI ID

61305

Good Scents ID

Not Available

References

General References

de Kraker JW, Franssen MC, Joerink M, de Groot A, Bouwmeester HJ: Biosynthesis of costunolide, dihydrocostunolide, and leucodin. Demonstration of cytochrome p450-catalyzed formation of the lactone ring present in sesquiterpene lactones of chicory. Plant Physiol. 2002 May;129(1):257-68. doi: 10.1104/pp.010957. [PubMed:12011356 ]

Showing NP-Card for Germacra-1(10),4,11(13)-trien-12-oic acid (NP0075367)

MOL for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

3D MOL for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

3D SDF for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

3D-SDF for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

PDB for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

3D PDB for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

SMILES for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

INCHI for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

Structure for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)

3D Structure for NP0075367 (Germacra-1(10),4,11(13)-trien-12-oic acid)