NP-MRD: Showing NP-Card for (+)-germacrene d (NP0188697)

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Record Information

Version

2.0

Created at

2022-09-04 05:03:58 UTC

Updated at

2022-09-04 05:03:58 UTC

NP-MRD ID

NP0188697

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-germacrene d

Description

(+)-Germacrene D 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. (+)-germacrene d is found in Dendropanax trifidus, Eunicea fusca, Jackiella javanica, Lessingianthus linearis, Marchantia quadrata, Pleiotaxis rugosa, Prumnopitys andina, Solidago canadensis, Taonia atomaria and Xanthium strumarium. (+)-germacrene d was first documented in 2022 (PMID: 36026582). Based on a literature review a small amount of articles have been published on (+)-germacrene D (PMID: 35981267) (PMID: 35895051) (PMID: 35889279).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 39  0  0  0  0  0  0  0  0999 V2000
   -1.8975   -3.4384   -0.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4823   -2.1824   -0.4547 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3979   -1.8718   -1.3389 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6993   -1.1884   -1.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0799   -0.5673    0.2003 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6185   -0.5973    0.3214 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2517    0.2409   -0.7664 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0601   -0.0625    1.6488 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6940    0.8685    0.3409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3355    1.3390   -0.6579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5137    1.8848    0.0497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3401    3.2311    0.7079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6423    1.2504    0.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8260   -0.0716   -0.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2279   -1.1506    0.3450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7232   -3.7127    0.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4540   -4.2725   -0.8193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5065   -2.2779   -2.3729 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4421   -1.0357   -1.8939 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7181   -1.1435    1.0799 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9232   -1.6610    0.2578 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8857    1.0630   -0.3294 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9431   -0.4171   -1.3364 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5081    0.6553   -1.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1230   -0.3633    1.7894 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0500    1.0532    1.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4968   -0.4791    2.5088 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2963    1.0493    1.3839 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5674    1.5734    0.2803 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0723    2.2167   -1.2507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5553    0.5730   -1.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8351    3.1355    1.6986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8578    3.9555    0.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2877    3.4661    0.8812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5283    1.6518    0.6370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4292   -0.1053   -1.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9257   -0.2996   -0.6813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0731   -1.6155    0.8920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5904   -0.6940    1.1131 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  8  1  0
  6  5  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 15  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  7 22  1  0
  7 23  1  0
  7 24  1  0
  6 21  1  0
  8 25  1  0
  8 26  1  0
  8 27  1  0
  5 20  1  1
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 12 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
M  END


  Mrv1652309042207032D          

 15 15  0  0  1  0            999 V2000
    1.9690    2.1275    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
    1.6990    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  1  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
    1.1589    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2293    0.9227    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  2  2  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  1  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  5  9  1  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
 11 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  2 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0188697

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@H]1CC\C(C)=C\CCC(=C)\C=C\1

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h7-8,10,12,15H,3,5-6,9,11H2,1-2,4H3/b10-8+,14-7+/t15-/m1/s1

> <INCHI_KEY>
GAIBLDCXCZKKJE-RGZOGPIRSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
25.890440392398986

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1E,6E,8R)-1-methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene

> <JCHEM_LOGP>
4.923184751333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
70.5495

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(+)-germacrene D

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       3.676   3.971   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   2.807   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.171   1.352   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.684   1.061   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.188  -0.394   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.700  -0.685   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.708   0.479   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.204  -2.140   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.180  -1.558   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -1.267   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.163   0.188   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.295   1.722   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.651   0.479   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.147   1.934   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.155   3.098   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    5   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    2                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
(1E,6E,8R)-1-Methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene	ChEBI
Germacrene D	MeSH
Germacrene D, (S-(e,e))-isomer	MeSH

Chemical Formula

C₁₅H₂₄

Average Mass

204.3570 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

(1E,6E,8R)-1-methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene

Traditional Name

(+)-germacrene D

CAS Registry Number

Not Available

SMILES

CC(C)[C@H]1CC\C(C)=C\CCC(=C)\C=C\1

InChI Identifier

InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h7-8,10,12,15H,3,5-6,9,11H2,1-2,4H3/b10-8+,14-7+/t15-/m1/s1

InChI Key

GAIBLDCXCZKKJE-RGZOGPIRSA-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
Dendropanax trifidus	LOTUS Database	35616633
Eunicea fusca	LOTUS Database	35616633
Jackiella javanica	LOTUS Database	35616633
Lessingianthus linearis	LOTUS Database	35616633
Marchantia quadrata	LOTUS Database	35616633
Pleiotaxis rugosa	LOTUS Database	35616633
Prumnopitys andina	LOTUS Database	35616633
Solidago canadensis	LOTUS Database	35616633
Taonia atomaria	LOTUS Database	35616633
Xanthium strumarium	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
Branched unsaturated hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

germacrene D (CHEBI:49046 )

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	4.92	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	70.55 m³·mol⁻¹	ChemAxon
Polarizability	25.89 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

Not Available

Chemspider ID

21865626

KEGG Compound ID

C19619

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24771782

PDB ID

Not Available

ChEBI ID

49046

Good Scents ID

Not Available

References

General References

Tian P, Zhang Y, Wang Z, Liu S, Chen Q, Hu H, Li D: Sex-Related Differences on Chemical Composition, Anatomy, Histochemistry, and Biological Activities of Juniperus rigida. Chem Biodivers. 2022 Sep;19(9):e202200404. doi: 10.1002/cbdv.202200404. Epub 2022 Aug 26. [PubMed:36026582 ]
Bernal FA, Matulevich JA, Corredor JA, Coy-Barrera E: GC/MS-Based Fingerprinting Reveals Two Chemotypes in the Leaf Essential Oils from Magnolia grandiflora Trees within The Urban Forestry of a Colombian Andean Plateau. Chem Biodivers. 2022 Sep;19(9):e202200448. doi: 10.1002/cbdv.202200448. Epub 2022 Sep 5. [PubMed:35981267 ]
Hamdi B, Peron G, Miara MD, Bouriah N, Flamini G, Maggi F, Sut S, Dall'Acqua S: Phytochemical analysis of Clinopodium candidissimum (Munby) Kuntze growing in Algeria by an integrated HS-SPME-GC-MS, NMR and HPLC-DAD-MS(n) approach: valorisation of an endemic natural source of bioactive compounds. Nat Prod Res. 2022 Jul 27:1-6. doi: 10.1080/14786419.2022.2104272. [PubMed:35895051 ]
Galvao AFC, Araujo MS, Silva VR, Santos LS, Dias RB, Rocha CAG, Soares MBP, Silva FMAD, Koolen HHF, Zengin G, Costa EV, Bezerra DP: Antitumor Effect of Guatteria olivacea R. E. Fr. (Annonaceae) Leaf Essential Oil in Liver Cancer. Molecules. 2022 Jul 9;27(14):4407. doi: 10.3390/molecules27144407. [PubMed:35889279 ]
LOTUS database [Link]

Showing NP-Card for (+)-germacrene d (NP0188697)

MOL for NP0188697 ((+)-germacrene d)

3D MOL for NP0188697 ((+)-germacrene d)

3D SDF for NP0188697 ((+)-germacrene d)

3D-SDF for NP0188697 ((+)-germacrene d)

PDB for NP0188697 ((+)-germacrene d)

3D PDB for NP0188697 ((+)-germacrene d)

SMILES for NP0188697 ((+)-germacrene d)

INCHI for NP0188697 ((+)-germacrene d)

Structure for NP0188697 ((+)-germacrene d)

3D Structure for NP0188697 ((+)-germacrene d)