NP-MRD: Showing NP-Card for (2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol (NP0304873)

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Record Information

Version

2.0

Created at

2022-09-10 20:15:55 UTC

Updated at

2022-09-10 20:15:55 UTC

NP-MRD ID

NP0304873

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol

Description

Germacrene D-4-ol 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. (2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol is found in Ajuga chamaepitys, Daniellia oliveri, Pinus sylvestris and Thulinella chrysantha. (2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol was first documented in 2019 (PMID: 30693926). Based on a literature review a small amount of articles have been published on germacrene D-4-ol (PMID: 35075577) (PMID: 32872359) (PMID: 32372353) (PMID: 32282967).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 42 42  0  0  0  0  0  0  0  0999 V2000
   -1.1040    2.9694    1.1670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1864    1.9358    0.0513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3270    1.3991   -0.3356 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6047    0.4120   -1.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8100   -0.8580   -1.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7606   -1.6219   -0.1091 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5568   -0.9552    1.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6106   -2.7680   -0.3583 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4812   -2.1484    0.3453 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7618   -1.7771    0.2640 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4030   -0.5967   -0.3627 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9497   -0.6478   -0.1479 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2793   -0.6928    1.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5362    0.5496   -0.8511 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9202    0.6409    0.3175 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1617    1.6094   -0.5389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2878    2.6788    1.8807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7947    3.9085    0.7024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0286    3.0037    1.7427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2074    1.7831    0.2328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6802    0.0655   -1.2782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6174    0.8544   -2.4119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8220   -0.7741   -1.8083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3445   -1.4739   -2.2038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5042   -0.5538    0.6546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8548   -1.8093    1.7098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9560   -0.3038    1.6541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4916   -3.0646   -1.2797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5897   -3.1244    0.9221 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5573   -2.4379    0.7429 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3829   -0.5785   -1.4687 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2857   -1.5442   -0.6803 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1409   -1.4131    1.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4490   -1.0275    1.9323 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6892    0.2857    1.6781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8391    1.3782   -0.9886 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9421    0.2931   -1.8519 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3767    0.9372   -0.2263 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7838    1.1466    0.8515 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2497    0.3984    1.1982 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1161    1.3661   -1.6106 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7960    2.5555   -0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 14  1  0
 12 11  1  0
 11 15  1  0
 15 16  1  0
 16  2  1  0
  2  1  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  6
  6  9  1  0
  9 10  2  0
 10 11  1  0
 13 33  1  0
 13 34  1  0
 13 35  1  0
 12 32  1  0
 14 36  1  0
 14 37  1  0
 14 38  1  0
 11 31  1  6
 15 39  1  0
 15 40  1  0
 16 41  1  0
 16 42  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  7 25  1  0
  7 26  1  0
  7 27  1  0
  8 28  1  0
  9 29  1  0
 10 30  1  0
M  END


  Mrv1652309102222152D          

 16 16  0  0  0  0            999 V2000
    1.9624    0.2878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3488    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4418    2.3288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2435    1.6344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7792   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5893   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1294    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8593   -1.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -0.8348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 11 15  1  0  0  0  0
 15 16  1  0  0  0  0
  2 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0304873

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C1CC\C(C)=C\CCC(C)(O)\C=C\1

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O/c1-12(2)14-8-7-13(3)6-5-10-15(4,16)11-9-14/h6,9,11-12,14,16H,5,7-8,10H2,1-4H3/b11-9+,13-6+

> <INCHI_KEY>
RHCTXHCNRLCYBN-BMCYRRRCSA-N

> <FORMULA>
C15H26O

> <MOLECULAR_WEIGHT>
222.372

> <EXACT_MASS>
222.198365457

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
27.224204298014644

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,7E)-1,7-dimethyl-4-(propan-2-yl)cyclodeca-2,7-dien-1-ol

> <JCHEM_LOGP>
4.033577067333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.586977272603132

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2298561409633901

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
72.3771

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2E,7E)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       3.663   0.537   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.163   0.188   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.651   0.479   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.147   1.934   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.155   3.098   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   2.807   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.691   4.347   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.188   3.051   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.171   1.352   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.684   1.061   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.188  -0.394   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.700  -0.685   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.708   0.479   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.204  -2.140   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.180  -1.558   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667  -1.267   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   15                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   11   16                                                       
CONECT   16   15    2                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
Germacra-1(10),5-dien-4-ol	ChEBI
Germacrene-D-4-ol	ChEBI

Chemical Formula

C₁₅H₂₆O

Average Mass

222.3720 Da

Monoisotopic Mass

222.19837 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(C)C1CC\C(C)=C\CCC(C)(O)\C=C\1

InChI Identifier

InChI=1S/C15H26O/c1-12(2)14-8-7-13(3)6-5-10-15(4,16)11-9-14/h6,9,11-12,14,16H,5,7-8,10H2,1-4H3/b11-9+,13-6+

InChI Key

RHCTXHCNRLCYBN-BMCYRRRCSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Ajuga chamaepitys	LOTUS Database	35616633
Daniellia oliveri	LOTUS Database	35616633
Pinus sylvestris	LOTUS Database	35616633
Thulinella chrysantha	LOTUS Database	35616633

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
Tertiary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00053255

Chemspider ID

10423135

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5352847

PDB ID

Not Available

ChEBI ID

141218

Good Scents ID

Not Available

References

General References

Sone M, Komatsu K, Zhu S, Cheng X, Ketphanh S, Kawahara N: Essential oil components in the seed masses of Amomum xanthioides and its related species from Southeast Asia and China. J Nat Med. 2022 Mar;76(2):435-450. doi: 10.1007/s11418-021-01599-7. Epub 2022 Jan 25. [PubMed:35075577 ]
Zheljazkov VD, Sikora V, Semerdjieva IB, Kacaniova M, Astatkie T, Dincheva I: Grinding and Fractionation during Distillation Alter Hemp Essential Oil Profile and Its Antimicrobial Activity. Molecules. 2020 Aug 28;25(17):3943. doi: 10.3390/molecules25173943. [PubMed:32872359 ]
Ammar S, Noui H, Djamel S, Madani S, Maggi F, Bruno M, Romano D, Canale A, Pavela R, Benelli G: Essential oils from three Algerian medicinal plants (Artemisia campestris, Pulicaria arabica, and Saccocalyx satureioides) as new botanical insecticides? Environ Sci Pollut Res Int. 2020 Jul;27(21):26594-26604. doi: 10.1007/s11356-020-09064-w. Epub 2020 May 5. [PubMed:32372353 ]
Karunanithi PS, Berrios DI, Wang S, Davis J, Shen T, Fiehn O, Maloof JN, Zerbe P: The foxtail millet (Setaria italica) terpene synthase gene family. Plant J. 2020 Jul;103(2):781-800. doi: 10.1111/tpj.14771. Epub 2020 May 3. [PubMed:32282967 ]
Burkhardt I, Kreuzenbeck NB, Beemelmanns C, Dickschat JS: Mechanistic characterization of three sesquiterpene synthases from the termite-associated fungus Termitomyces. Org Biomol Chem. 2019 Mar 27;17(13):3348-3355. doi: 10.1039/c8ob02744g. [PubMed:30693926 ]
LOTUS database [Link]

Showing NP-Card for (2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol (NP0304873)

MOL for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

3D MOL for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

3D SDF for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

3D-SDF for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

PDB for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

3D PDB for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

SMILES for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

INCHI for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

Structure for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)

3D Structure for NP0304873 ((2e,7e)-4-isopropyl-1,7-dimethylcyclodeca-2,7-dien-1-ol)