NP-MRD: Showing NP-Card for (+) germacrene a (NP0271528)

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Record Information

Version

1.0

Created at

2022-09-08 17:51:33 UTC

Updated at

2022-09-08 17:51:33 UTC

NP-MRD ID

NP0271528

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+) germacrene a

Description

(+)-Germacrene A 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. Thus, (+)-germacrene a is considered to be an isoprenoid. (+) germacrene a is found in Azadirachta indica, Betonica macrantha, Cichorium intybus, Fitchia speciosa, Frullania tamarisci, Lantana camara, Salvia syriaca, Santolina insularis and Smallanthus uvedalia. It was first documented in 2022 (PMID: 36035671). Based on a literature review a significant number of articles have been published on (+)-germacrene A (PMID: 35869098) (PMID: 35723427) (PMID: 35696915) (PMID: 35630799).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 39  0  0  0  0  0  0  0  0999 V2000
    3.0439   -0.2002   -1.5662 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5919   -0.4090   -0.3523 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4880   -1.0094    0.6698 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2036   -0.0715    0.0680 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4529   -1.2990    0.5440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6603   -1.6729   -0.3750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9457   -1.5013   -0.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0162   -1.8941   -1.0529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4153   -0.9057    1.1970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0478    0.5191    1.3604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7179    1.0798    0.0284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6493    1.8211   -0.2067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3882    2.3546   -1.5889 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3000    2.1375    0.8819 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2670    1.0103    1.0862 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0503   -0.4594   -1.8216 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4030    0.2330   -2.3099 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2629   -0.5759    1.6502 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3620   -2.1101    0.7537 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5722   -0.8676    0.3889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6757    0.2703   -0.8493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1111   -1.1983    1.5922 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1868   -2.1324    0.5405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3509   -2.1084   -1.3208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5840   -2.1469   -2.0620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5703   -2.7846   -0.6361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7632   -1.1239   -1.2232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9157   -1.4818    2.0193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4877   -1.0476    1.3492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2534    0.7062    2.1095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9386    1.0679    1.7264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4064    0.8556   -0.7816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0072    3.2651   -1.6931 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6772    2.6025   -1.6696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6204    1.6030   -2.3691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2178    2.4378    1.8187 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8745    3.0358    0.5769 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1413    0.5681    2.1051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2920    1.4324    1.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  3
  2  4  1  0
  4 15  1  0
 15 14  1  0
 14 12  1  0
 12 13  1  0
 12 11  2  0
 11 10  1  0
 10  9  1  0
  9  7  1  0
  7  8  1  0
  7  6  2  0
  6  5  1  0
  5  4  1  0
  3 18  1  0
  3 19  1  0
  3 20  1  0
  1 16  1  0
  1 17  1  0
  4 21  1  6
 15 38  1  0
 15 39  1  0
 14 36  1  0
 14 37  1  0
 13 33  1  0
 13 34  1  0
 13 35  1  0
 11 32  1  0
 10 30  1  0
 10 31  1  0
  9 28  1  0
  9 29  1  0
  8 25  1  0
  8 26  1  0
  8 27  1  0
  6 24  1  0
  5 22  1  0
  5 23  1  0
M  END

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       1.928   6.109   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.037   5.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.517   5.468   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   3.546   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.777   2.478   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.407   0.984   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.517  -0.084   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.996   0.343   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.147  -1.579   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -2.006   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.558  -0.938   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.928   0.556   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.874   1.772   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.818   1.624   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.188   3.119   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   15                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    4                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
(+)-(R)-Germacrene a	ChEBI
(1E,5E,8R)-8-Isopropenyl-1,5-dimethylcyclodeca-1,5-diene	ChEBI
GERMACRENE a	ChEBI

Chemical Formula

C₁₅H₂₄

Average Mass

204.3570 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

(1E,5E,8R)-1,5-dimethyl-8-(prop-1-en-2-yl)cyclodeca-1,5-diene

Traditional Name

germacrene a

CAS Registry Number

Not Available

SMILES

CC(=C)[C@@H]1CC\C(C)=C\CC\C(C)=C\C1

InChI Identifier

InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h6,9,15H,1,5,7-8,10-11H2,2-4H3/b13-6+,14-9+/t15-/m1/s1

InChI Key

XMRKUJJDDKYUHV-DFSVIBJJSA-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
Azadirachta indica	LOTUS Database	35616633
Betonica macrantha	LOTUS Database	35616633
Cichorium intybus	LOTUS Database	35616633
Fitchia speciosa	LOTUS Database	35616633
Frullania tamarisci	LOTUS Database	35616633
Lantana camara	LOTUS Database	35616633
Salvia syriaca	LOTUS Database	35616633
Santolina insularis	LOTUS Database	35616633
Smallanthus uvedalia	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 A (CHEBI:41595 )
Germacrane sesquiterpenoids (LMPR0103090001 )

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	4.88	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	70.28 m³·mol⁻¹	ChemAxon
Polarizability	25.37 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

C00036308

Chemspider ID

7827628

KEGG Compound ID

C16141

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9548705

PDB ID

Not Available

ChEBI ID

41595

Good Scents ID

Not Available

References

General References

Chen R, Liu Y, Chen S, Wang M, Zhu Y, Hu T, Wei Q, Yin X, Xie T: Protein Engineering of a Germacrene A Synthase From Lactuca sativa and Its Application in High Productivity of Germacrene A in Escherichia coli. Front Plant Sci. 2022 Aug 11;13:932966. doi: 10.3389/fpls.2022.932966. eCollection 2022. [PubMed:36035671 ]
Mir WR, Bhat BA, Rather MA, Muzamil S, Almilaibary A, Alkhanani M, Mir MA: Molecular docking analysis and evaluation of the antimicrobial properties of the constituents of Geranium wallichianum D. Don ex Sweet from Kashmir Himalaya. Sci Rep. 2022 Jul 22;12(1):12547. doi: 10.1038/s41598-022-16102-9. [PubMed:35869098 ]
Shi Y, Dong T, Zeng B, Yao M, Wang Y, Xie Z, Xiao W, Yuan Y: Production of Plant Sesquiterpene Lactone Parthenolide in the Yeast Cell Factory. ACS Synth Biol. 2022 Jul 15;11(7):2473-2483. doi: 10.1021/acssynbio.2c00132. Epub 2022 Jun 20. [PubMed:35723427 ]
Hong CY, Tsao NW, Wang SY, Chu FH: Cloning and functional characterization of three sesquiterpene synthase genes from Chamaecyparis formosensis Matsumura. Plant Sci. 2022 Aug;321:111315. doi: 10.1016/j.plantsci.2022.111315. Epub 2022 May 18. [PubMed:35696915 ]
Xie DM, Zhang Q, Xin LK, Wang GK, Liu CB, Qin MJ: Cloning and Functional Characterization of Two Germacrene A Oxidases Isolated from Xanthium sibiricum. Molecules. 2022 May 22;27(10):3322. doi: 10.3390/molecules27103322. [PubMed:35630799 ]
LOTUS database [Link]

Showing NP-Card for (+) germacrene a (NP0271528)

MOL for NP0271528 ((+) germacrene a)

3D MOL for NP0271528 ((+) germacrene a)

3D SDF for NP0271528 ((+) germacrene a)

3D-SDF for NP0271528 ((+) germacrene a)

PDB for NP0271528 ((+) germacrene a)

3D PDB for NP0271528 ((+) germacrene a)

SMILES for NP0271528 ((+) germacrene a)

INCHI for NP0271528 ((+) germacrene a)

Structure for NP0271528 ((+) germacrene a)

3D Structure for NP0271528 ((+) germacrene a)