NP-MRD: Showing NP-Card for (-)-trans-α-bergamotene (NP0305912)

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Record Information

Version

2.0

Created at

2022-09-10 22:04:53 UTC

Updated at

2022-09-10 22:04:53 UTC

NP-MRD ID

NP0305912

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-trans-α-bergamotene

Description

(-)-Exo-alpha-bergamotene belongs to the class of organic compounds known as bicyclic monoterpenoids. (-)-trans-α-bergamotene is found in Achillea abrotanoides, Aframomum angustifolium, Aristolochia triangularis, Atalantia buxifolia, Cannabis sativa, Cinnamomum burmannii, Cinnamomum verum, Cistus incanus, Citrus aurantiifolia, Citrus limon, Citrus medica, Copaifera duckei, Cuminum cyminum, Erigeron canadensis, Eupatorium capillifolium, Hedychium spicatum, Heterotheca subaxillaris, Mesosphaerum suaveolens, Lantana camara, Lavandula angustifolia, Lavandula latifolia, Nepeta glomerulosa, Osyris quadripartita, Persea americana, Phyla dulcis, Pinus merkusii, Piper guineense, Salvia cuspidata, Salvia dorisiana, Solidago canadensis, Spondias mombin, Tambourissa leptophylla, Trachyspermum anethifolium, Vitex agnus-castus and Widdringtonia whytei. (-)-trans-α-bergamotene was first documented in 2006 (PMID: 16418295). These are monoterpenoids containing exactly 2 rings, which are fused to each other (-)-exo-alpha-bergamotene is possibly neutral (PMID: 17662687).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
    5.1424   -0.8420    0.0545 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8217   -0.1960   -0.1205 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6586    0.8296   -1.1787 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8248   -0.5534    0.6735 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5105    0.1007    0.4870 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4207   -0.8856    0.1504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8586   -0.1002   -0.0157 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7029    0.9092   -1.1199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3736    0.3877    1.2987 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3491    1.5223    1.0801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3602    1.0468    0.0642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2230   -0.1201   -0.5270 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1658   -0.5575   -1.5600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0956   -0.9706   -0.1191 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1166   -0.9487    1.4193 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9701   -0.0852    0.1250 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3713   -1.4101   -0.8886 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1779   -1.5042    0.9376 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6144    1.0036   -1.6694 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8799    0.4227   -1.8855 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3271    1.8110   -0.7556 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9769   -1.3119    1.4433 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5803    0.8704   -0.2845 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2524    0.5453    1.4838 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6584   -1.4680   -0.7692 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3546   -1.6147    0.9683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3387    1.8538   -0.7093 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0359    0.5251   -1.8369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6339    1.0965   -1.6887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6680    0.5270    2.1240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8869    1.7737    2.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7762    2.3817    0.6881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1841    1.7074   -0.1434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7802   -1.4984   -2.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1635   -0.8632   -1.1435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2873    0.1656   -2.3920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9805   -1.9464   -0.5702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1425   -0.8579    1.8247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4908   -1.7458    1.8165 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  7  6  1  1
  7  8  1  0
  7  9  1  0
  9 15  1  0
 15 14  1  0
 14 12  1  0
 12 13  1  0
 12 11  2  0
 11 10  1  0
 14  7  1  0
 10  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  8 27  1  0
  8 28  1  0
  8 29  1  0
  9 30  1  1
 15 38  1  0
 15 39  1  0
 14 37  1  1
 13 34  1  0
 13 35  1  0
 13 36  1  0
 11 33  1  0
 10 31  1  0
 10 32  1  0
M  END


  Mrv1652303192001303D          

 15 16  0  0  0  0            999 V2000
    3.4686    1.6720   -0.0927 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2033   -0.1996    0.3160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4839    1.8673    1.0418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6294   -1.2665    1.4411 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5011   -0.3378   -0.5769 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8947   -0.7176   -0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6210   -0.2012   -0.2024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9719   -1.2725   -0.9974 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5319   -0.8532    0.3994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3286    0.4155   -1.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7912    0.2155   -0.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8766    0.7818    0.2469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4825   -1.0394   -1.0468 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4243    0.7621   -0.0688 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8989   -0.5981    0.2735 C   0  0  1  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  2 11  1  0  0  0  0
  3 12  1  0  0  0  0
 15  4  1  1  0  0  0
  5  6  1  0  0  0  0
  5  9  1  0  0  0  0
  6 11  2  3  0  0  0
  7  8  1  0  0  0  0
  7 12  2  0  0  0  0
 13  8  1  1  0  0  0
  9 15  1  0  0  0  0
 10 13  1  0  0  0  0
 14 10  1  6  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0305912

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC[C@]1(C)[C@@H]2C[C@H]1C(C)=CC2

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-11(2)6-5-9-15(4)13-8-7-12(3)14(15)10-13/h6-7,13-14H,5,8-10H2,1-4H3/t13-,14-,15+/m0/s1

> <INCHI_KEY>
YMBFCQPIMVLNIU-SOUVJXGZSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.450971158955333

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,5S,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene

> <ALOGPS_LOGP>
5.91

> <JCHEM_LOGP>
4.461375721333334

> <ALOGPS_LOGS>
-4.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
68.5249

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.82e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-trans-α-bergamotene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 19-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-MAR-20         0                                  
HETATM    1  C   UNK     0       3.469   1.672  -0.093  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.203  -0.200   0.316  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.484   1.867   1.042  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.629  -1.266   1.441  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.501  -0.338  -0.577  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.895  -0.718  -0.243  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.621  -0.201  -0.202  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.972  -1.272  -0.997  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.532  -0.853   0.399  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.329   0.416  -1.515  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.791   0.216  -0.022  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.877   0.782   0.247  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.482  -1.039  -1.047  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.424   0.762  -0.069  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.899  -0.598   0.274  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   15                                                            
CONECT    5    6    9                                                       
CONECT    6    5   11                                                       
CONECT    7    8   12                                                       
CONECT    8    7   13                                                       
CONECT    9    5   15                                                       
CONECT   10   13   14                                                       
CONECT   11    1    2    6                                                  
CONECT   12    3    7   14                                                  
CONECT   13    8   10   15                                                  
CONECT   14   10   12   15                                                  
CONECT   15    4    9   13   14                                             
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Value	Source
(-)-trans-alpha-Bergamotene	ChEBI
(-)-trans-a-Bergamotene	Generator
(-)-trans-Α-bergamotene	Generator
(-)-exo-a-Bergamotene	Generator
(-)-exo-Α-bergamotene	Generator
alpha-Bergamotene	MeSH
cis-alpha-Bergamotene	MeSH

Chemical Formula

C₁₅H₂₄

Average Mass

204.3570 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

(1S,5S,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene

Traditional Name

(-)-trans-α-bergamotene

CAS Registry Number

Not Available

SMILES

CC(C)=CCC[C@]1(C)[C@@H]2C[C@H]1C(C)=CC2

InChI Identifier

InChI=1S/C15H24/c1-11(2)6-5-9-15(4)13-8-7-12(3)14(15)10-13/h6-7,13-14H,5,8-10H2,1-4H3/t13-,14-,15+/m0/s1

InChI Key

YMBFCQPIMVLNIU-SOUVJXGZSA-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
Achillea abrotanoides	LOTUS Database	35616633
Aframomum angustifolium	LOTUS Database	35616633
Aristolochia triangularis	LOTUS Database	35616633
Atalantia buxifolia	LOTUS Database	35616633
Cannabis sativa	LOTUS Database	35616633
Cinnamomum burmanni	LOTUS Database	35616633
Cinnamomum verum	LOTUS Database	35616633
Cistus incanus	LOTUS Database	35616633
Citrus aurantiifolia	LOTUS Database	35616633
Citrus limon	LOTUS Database	35616633
Citrus medica	LOTUS Database	35616633
Copaifera duckei	LOTUS Database	35616633
Cuminum cyminum	LOTUS Database	35616633
Erigeron canadensis	LOTUS Database	35616633
Eupatorium capillifolium	LOTUS Database	35616633
Hedychium spicatum	LOTUS Database	35616633
Heterotheca subaxillaris	LOTUS Database	35616633
Hyptis suaveolens	LOTUS Database	35616633
Lantana camara	LOTUS Database	35616633
Lavandula angustifolia	LOTUS Database	35616633
Lavandula latifolia	LOTUS Database	35616633
Nepeta glomerulosa	LOTUS Database	35616633
Osyris quadripartita	LOTUS Database	35616633
Persea americana	LOTUS Database	35616633
Phyla dulcis	LOTUS Database	35616633
Pinus merkusii	LOTUS Database	35616633
Piper guineense	LOTUS Database	35616633
Salvia cuspidata	LOTUS Database	35616633
Salvia dorisiana	LOTUS Database	35616633
Solidago canadensis	LOTUS Database	35616633
Spondias mombin	LOTUS Database	35616633
Tambourissa leptophylla	LOTUS Database	35616633
Trachyspermum anethifolium	LOTUS Database	35616633
Vitex agnus-castus	LOTUS Database	35616633
Widdringtonia whytei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Bicyclic monoterpenoids

Alternative Parents

Substituents

Pinane monoterpenoid
Bicyclic monoterpenoid
Branched unsaturated hydrocarbon
Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

alpha-bergamotene (CHEBI:62756 )

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	5.91	ALOGPS
logP	4.46	ChemAxon
logS	-4.5	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	68.52 m³·mol⁻¹	ChemAxon
Polarizability	26.45 Å³	ChemAxon
Number of Rings	2	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6429302

PDB ID

Not Available

ChEBI ID

62756

Good Scents ID

Not Available

References

General References

Schnee C, Kollner TG, Held M, Turlings TC, Gershenzon J, Degenhardt J: The products of a single maize sesquiterpene synthase form a volatile defense signal that attracts natural enemies of maize herbivores. Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):1129-34. doi: 10.1073/pnas.0508027103. Epub 2006 Jan 17. [PubMed:16418295 ]
Landmann C, Fink B, Festner M, Dregus M, Engel KH, Schwab W: Cloning and functional characterization of three terpene synthases from lavender (Lavandula angustifolia). Arch Biochem Biophys. 2007 Sep 15;465(2):417-29. doi: 10.1016/j.abb.2007.06.011. Epub 2007 Jun 26. [PubMed:17662687 ]
LOTUS database [Link]

Showing NP-Card for (-)-trans-α-bergamotene (NP0305912)

MOL for NP0305912 ((-)-trans-α-bergamotene)

3D MOL for NP0305912 ((-)-trans-α-bergamotene)

3D SDF for NP0305912 ((-)-trans-α-bergamotene)

3D-SDF for NP0305912 ((-)-trans-α-bergamotene)

PDB for NP0305912 ((-)-trans-α-bergamotene)

3D PDB for NP0305912 ((-)-trans-α-bergamotene)

SMILES for NP0305912 ((-)-trans-α-bergamotene)

INCHI for NP0305912 ((-)-trans-α-bergamotene)

Structure for NP0305912 ((-)-trans-α-bergamotene)

3D Structure for NP0305912 ((-)-trans-α-bergamotene)