NP-MRD: Showing NP-Card for (-)-endo-α-bergamotene (NP0247040)

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Record Information

Version

2.0

Created at

2022-09-07 08:42:38 UTC

Updated at

2022-09-07 08:42:39 UTC

NP-MRD ID

NP0247040

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-endo-α-bergamotene

Description

(-)-Endo-alpha-bergamotene, also known as (1S,5S,6S)-alpha-bergamotene, belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other. (-)-endo-α-bergamotene is found in Achyrospermum africanum, Alpinia latilabris, Arum maculatum, Citrus hystrix, Erigeron canadensis, Gossypium hirsutum, Hamamelis virginiana, Helichrysum italicum, Heterotheca subaxillaris, Isocoma tenuisecta, Gymnomitrion alpinum, Mosla cavaleriei, Osyris quadripartita, Pelargonium endlicherianum, Pimpinella anisum, Solidago canadensis, Spondias mombin, Tambourissa leptophylla, Tanacetum longifolium, Vitex agnus-castus and Widdringtonia whytei. (-)-endo-α-bergamotene was first documented in 2009 (PMID: 19155349). Based on a literature review a small amount of articles have been published on (-)-endo-alpha-bergamotene (PMID: 35003184) (PMID: 22951817).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
    3.3157   -0.9413    0.7296 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3345    0.5394    0.5396 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3724    1.4008    1.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4002    1.1109   -0.2073 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3253    0.2837   -0.8623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0394    0.7609   -0.3470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0723   -0.0768   -1.0155 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0011    0.0771   -2.5132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1779   -1.5114   -0.5695 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9975   -1.6896    0.9014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8690   -0.6877    1.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5133    0.2331    0.9141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2350    1.3604    1.5438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4984    0.1112   -0.5546 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6841   -1.3874   -0.8445 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3778   -1.4642   -0.2454 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4014   -1.2309    1.2609 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2041   -1.2247    1.3630 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0817    1.7719    0.3929 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9144    0.8159    1.9252 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8646    2.2351    1.6677 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4017    2.1920   -0.3548 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687    0.4199   -1.9483 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4875   -0.7688   -0.5642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1728    1.8203   -0.5568 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0128    0.6445    0.7531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7153    1.1216   -2.7668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9745   -0.1171   -3.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2244   -0.5720   -2.9548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6735   -2.2501   -1.2077 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0394   -1.6462    1.2359 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3882   -2.7109    1.1603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9301   -0.7655    2.6764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7585    1.6686    2.4839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2944    1.0182    1.6942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3034    2.1989    0.8058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1272    0.7767   -1.1346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9658   -1.6005   -1.8771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2862   -1.9159   -0.0768 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  6
 15 38  1  0
 15 39  1  0
 14 37  1  6
 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


  Mrv1652309072210422D          

 15 16  0  0  1  0            999 V2000
   -1.6569    3.3928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0249    2.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2496    3.1447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1681    2.0501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5362    1.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6794    0.7073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0474    0.1770    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6794   -0.3533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3651    0.8915    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1901    0.8915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6026    0.1770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1901   -0.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6026   -1.2519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3651   -0.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5437    0.1770    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
  2  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  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  6  0  0  0
  9 15  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0247040

> <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-KKUMJFAQSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.380938615166677

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
4.461375721333334

> <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

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

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.093   6.333   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.913   5.343   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.466   5.870   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.181   3.827   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.001   2.837   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.268   1.320   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.089   0.330   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.268  -0.659   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.681   1.664   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.221   1.664   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.991   0.330   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.221  -1.003   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.991  -2.337   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.681  -1.003   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.015   0.330   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   14                                             
CONECT    8    7                                                            
CONECT    9    7   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    7   15                                                  
CONECT   15   14    9                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Value	Source
(1S,5S,6S)-alpha-Bergamotene	ChEBI
(1S,5S,6S)-a-Bergamotene	Generator
(1S,5S,6S)-Α-bergamotene	Generator
(-)-endo-a-Bergamotene	Generator
(-)-endo-Α-bergamotene	Generator
alpha-Bergamotene	MeSH
trans-alpha-Bergamotene	MeSH
cis-alpha-Bergamotene	MeSH

Chemical Formula

C₁₅H₂₄

Average Mass

204.3570 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

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

Traditional Name

(-)-endo-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-KKUMJFAQSA-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
Achyrospermum africanum	LOTUS Database	35616633
Alpinia latilabris	LOTUS Database	35616633
Arum maculatum	LOTUS Database	35616633
Citrus hystrix	LOTUS Database	35616633
Erigeron canadensis	LOTUS Database	35616633
Gossypium hirsutum	LOTUS Database	35616633
Hamamelis virginiana	LOTUS Database	35616633
Helichrysum italicum	LOTUS Database	35616633
Heterotheca subaxillaris	LOTUS Database	35616633
Isocoma tenuisecta	LOTUS Database	35616633
Marsupella alpina	LOTUS Database	35616633
Mosla cavaleriei	LOTUS Database	35616633
Osyris quadripartita	LOTUS Database	35616633
Pelargonium endlicherianum	LOTUS Database	35616633
Pimpinella anisum	LOTUS Database	35616633
Solidago canadensis	LOTUS Database	35616633
Spondias mombin	LOTUS Database	35616633
Tambourissa leptophylla	LOTUS Database	35616633
Tanacetum longifolium	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:61679 )

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	4.46	ChemAxon
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	26.38 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

10379953

KEGG Compound ID

C19735

BioCyc ID

CPD-8849

BiGG ID

Not Available

Wikipedia Link

Bergamotene

METLIN ID

Not Available

PubChem Compound

6429303

PDB ID

Not Available

ChEBI ID

61679

Good Scents ID

Not Available

References

General References

Wang F, Park YL, Gutensohn M: Epidermis-Specific Metabolic Engineering of Sesquiterpene Formation in Tomato Affects the Performance of Potato Aphid Macrosiphum euphorbiae. Front Plant Sci. 2021 Dec 22;12:793313. doi: 10.3389/fpls.2021.793313. eCollection 2021. [PubMed:35003184 ]
Jindal G, Sunoj RB: Revisiting sesquiterpene biosynthetic pathways leading to santalene and its analogues: a comprehensive mechanistic study. Org Biomol Chem. 2012 Oct 21;10(39):7996-8006. doi: 10.1039/c2ob26027a. [PubMed:22951817 ]
Sallaud C, Rontein D, Onillon S, Jabes F, Duffe P, Giacalone C, Thoraval S, Escoffier C, Herbette G, Leonhardt N, Causse M, Tissier A: A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites. Plant Cell. 2009 Jan;21(1):301-17. doi: 10.1105/tpc.107.057885. Epub 2009 Jan 20. [PubMed:19155349 ]
LOTUS database [Link]

Showing NP-Card for (-)-endo-α-bergamotene (NP0247040)

MOL for NP0247040 ((-)-endo-α-bergamotene)

3D MOL for NP0247040 ((-)-endo-α-bergamotene)

3D SDF for NP0247040 ((-)-endo-α-bergamotene)

3D-SDF for NP0247040 ((-)-endo-α-bergamotene)

PDB for NP0247040 ((-)-endo-α-bergamotene)

3D PDB for NP0247040 ((-)-endo-α-bergamotene)

SMILES for NP0247040 ((-)-endo-α-bergamotene)

INCHI for NP0247040 ((-)-endo-α-bergamotene)

Structure for NP0247040 ((-)-endo-α-bergamotene)

3D Structure for NP0247040 ((-)-endo-α-bergamotene)