NP-MRD: Showing NP-Card for (+)-endo-β-bergamotene (NP0265726)

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Record Information

Version

2.0

Created at

2022-09-08 09:48:50 UTC

Updated at

2022-09-08 09:48:50 UTC

NP-MRD ID

NP0265726

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-endo-β-bergamotene

Description

(+)-Endo-beta-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-β-bergamotene is found in Asarum fauriei, Citrus limon, Encelia canescens, Mesosphaerum suaveolens and Solidago canadensis. (+)-endo-β-bergamotene was first documented in 2009 (PMID: 19155349). Based on a literature review very few articles have been published on (+)-endo-beta-bergamotene (PMID: 35003184).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
   -3.9139    0.6571    1.1729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8947    0.1146    0.5572 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4771   -1.2675    0.8791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2347   -1.6718    0.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6997   -0.6074   -0.7853 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8971   -0.1228   -1.6225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1435    0.8531   -0.4600 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6322    0.7662   -0.2320 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0085    1.7372   -1.2008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2006    0.9904    1.1651 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2547    0.8737    1.4521 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8739   -0.4247    1.1722 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8798   -0.5391    0.3257 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4965    0.5771   -0.4250 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5043   -1.8982    0.0551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2013    1.6723    0.9199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5083    0.1603    1.9346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3485   -1.9470    0.6470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3287   -1.4169    1.9852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4933   -2.1734    0.7542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5736   -2.5035   -0.5891 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1478   -0.9513   -1.4000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7099   -0.8755   -1.7040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6343    0.3516   -2.5637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5147    1.8207   -0.7792 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4967    2.5285   -0.5993 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7117    1.2263   -1.8908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7221    2.2612   -1.8472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4789    2.0562    1.4244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7549    0.3849    1.9157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664    1.6712    0.9797 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4255    1.0505    2.5632 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5108   -1.3094    1.6677 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2553    1.0321    0.2732 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0957    0.2081   -1.2933 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8222    1.3560   -0.7652 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8978   -1.9464   -0.9809 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3634   -1.9947    0.7378 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7510   -2.6998    0.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 15  1  0
 13 12  2  3
 12 11  1  0
 11 10  1  0
  8 10  1  1
  8  9  1  0
  8  5  1  0
  5  6  1  0
  6  7  1  0
  7  2  1  0
  2  1  2  3
  2  3  1  0
  3  4  1  0
  7  8  1  0
  4  5  1  0
 14 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 15 39  1  0
 12 33  1  0
 11 31  1  0
 11 32  1  0
 10 29  1  0
 10 30  1  0
  9 26  1  0
  9 27  1  0
  9 28  1  0
  5 22  1  6
  6 23  1  0
  6 24  1  0
  7 25  1  6
  1 16  1  0
  1 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
M  END


  Mrv1652309082211482D          

 15 16  0  0  1  0            999 V2000
    2.5423    1.5837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1267    0.8710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5362    0.1547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1206   -0.5580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2957   -0.5544    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2326    0.1301    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3017    0.8745    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8862    0.1618    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1594    0.5522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1561   -0.2224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5416    0.2177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2717   -0.1665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9695    0.2737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6996   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9372    1.0981    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  7  6  1  1  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0265726

> <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/h6,13-14H,3,5,7-10H2,1-2,4H3/t13-,14-,15-/m0/s1

> <INCHI_KEY>
DGZBGCMPRYFWFF-KKUMJFAQSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.27656861825099

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,5S,6S)-6-methyl-2-methylidene-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]heptane

> <JCHEM_LOGP>
4.519309391666669

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
67.4524

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(+)-endo-β-bergamotene

> <JCHEM_VEBER_RULE>
1

$$$$

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       4.746   2.956   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.970   1.626   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.734   0.289   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.959  -1.042   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.419  -1.035   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.301   0.243   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.430   1.632   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.654   0.302   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.298   1.031   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.291  -0.415   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.011   0.406   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.374  -0.311   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.676   0.511   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.039  -0.206   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.616   2.050   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7    5    9   10                                             
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Value	Source
(+)-endo-b-Bergamotene	Generator
(+)-endo-Β-bergamotene	Generator

Chemical Formula

C₁₅H₂₄

Average Mass

204.3570 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

(1S,5S,6S)-6-methyl-2-methylidene-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]heptane

Traditional Name

(+)-endo-β-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/h6,13-14H,3,5,7-10H2,1-2,4H3/t13-,14-,15-/m0/s1

InChI Key

DGZBGCMPRYFWFF-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
Asarum fauriei	LOTUS Database	35616633
Citrus limon	LOTUS Database	35616633
Encelia canescens	LOTUS Database	35616633
Hyptis suaveolens	LOTUS Database	35616633
Solidago canadensis	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

bridged compound (CHEBI:61678 )
sesquiterpene (CHEBI:61678 )

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	4.52	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	67.45 m³·mol⁻¹	ChemAxon
Polarizability	26.28 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

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Bergamotene

METLIN ID

Not Available

PubChem Compound

12300073

PDB ID

Not Available

ChEBI ID

61678

Good Scents ID

rw1384441

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 ]
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-β-bergamotene (NP0265726)

MOL for NP0265726 ((+)-endo-β-bergamotene)

3D MOL for NP0265726 ((+)-endo-β-bergamotene)

3D SDF for NP0265726 ((+)-endo-β-bergamotene)

3D-SDF for NP0265726 ((+)-endo-β-bergamotene)

PDB for NP0265726 ((+)-endo-β-bergamotene)

3D PDB for NP0265726 ((+)-endo-β-bergamotene)

SMILES for NP0265726 ((+)-endo-β-bergamotene)

INCHI for NP0265726 ((+)-endo-β-bergamotene)

Structure for NP0265726 ((+)-endo-β-bergamotene)

3D Structure for NP0265726 ((+)-endo-β-bergamotene)