NP-MRD: Showing NP-Card for Bergamotene F (NP0333700)

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Record Information

Version

2.0

Created at

2024-08-06 08:01:35 UTC

Updated at

2026-02-28 08:02:21 UTC

NP-MRD ID

NP0333700

Natural Product DOI

https://doi.org/10.57994/3179

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Bergamotene F

Description

Bergamotene F belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol. Bergamotene F was first documented in 2024 (PMID: 39623525). Based on a literature review very few articles have been published on Bergamotene F.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 04202310352D          

 28 30  0  0  1  0            999 V2000
   -0.6794   -0.3533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0474    0.1770    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3651    0.8915    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
    1.1901    0.8915    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
   -1.4547    0.4251    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0867    0.9554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8619    0.6733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0052   -0.1392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4939    1.2036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3651   -0.5375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1901   -0.5375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0468   -1.3499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9653   -0.8196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1086   -1.6321    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8838   -1.9143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0271   -2.7267    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8023   -3.0089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4343   -2.4786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3951   -3.2570    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5384   -4.0695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6198   -2.9749    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9879   -3.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4766   -2.1624    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7013   -1.8802    0.0000 O   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
    2.4276    0.1770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12  4  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 16 15  1  6  0  0  0
 16 17  1  0  0  0  0
 18 17  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 21 18  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 16  1  0  0  0  0
 25 26  1  1  0  0  0
 13 27  1  0  0  0  0
  5 27  1  0  0  0  0
 27 28  2  0  0  0  0
M  END


  Mrv2104 04202310352D          

 28 30  0  0  1  0            999 V2000
   -0.6794   -0.3533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0474    0.1770    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3651    0.8915    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
    1.1901    0.8915    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
   -1.4547    0.4251    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0867    0.9554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8619    0.6733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0052   -0.1392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4939    1.2036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3651   -0.5375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1901   -0.5375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0468   -1.3499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9653   -0.8196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1086   -1.6321    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8838   -1.9143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0271   -2.7267    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8023   -3.0089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4343   -2.4786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3951   -3.2570    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5384   -4.0695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6198   -2.9749    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9879   -3.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4766   -2.1624    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7013   -1.8802    0.0000 O   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
    2.4276    0.1770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12  4  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 16 15  1  6  0  0  0
 16 17  1  0  0  0  0
 18 17  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 21 18  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 16  1  0  0  0  0
 25 26  1  1  0  0  0
 13 27  1  0  0  0  0
  5 27  1  0  0  0  0
 27 28  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0333700

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC[C@]1(C)[C@@H]2C[C@H]1[C@@](C)(O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(=O)C2

> <INCHI_IDENTIFIER>
InChI=1S/C21H34O7/c1-11(2)6-5-7-20(3)12-8-14(20)21(4,15(23)9-12)28-19-18(26)17(25)16(24)13(10-22)27-19/h6,12-14,16-19,22,24-26H,5,7-10H2,1-4H3/t12-,13-,14-,16-,17+,18-,19+,20-,21-/m1/s1

> <INCHI_KEY>
VGDXREUUIOCSAE-JRWWIKKGSA-N

> <FORMULA>
C21H34O7

> <MOLECULAR_WEIGHT>
398.496

> <EXACT_MASS>
398.230453435

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
43.65095489416463

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,5R,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}bicyclo[3.1.1]heptan-3-one

> <JCHEM_LOGP>
1.269536430666667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.199662485889089

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.209462421575923

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083868457077

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
102.30949999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5R,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}bicyclo[3.1.1]heptan-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-23         0                                  
HETATM    1  C   UNK     0      -1.268  -0.659   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.089   0.330   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.681   1.664   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.015   0.330   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.221   1.664   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      -2.715   0.794   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.895   1.784   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.342   1.257   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.610  -0.260   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -6.522   2.247   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.681  -1.003   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.221  -1.003   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.954  -2.520   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.669  -1.530   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.936  -3.047   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.383  -3.573   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       5.651  -5.090   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.098  -5.617   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.277  -4.627   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.471  -6.080   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.738  -7.596   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.024  -5.553   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.844  -6.543   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.756  -4.036   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.309  -3.510   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.991   0.330   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       4.531   0.330   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6   12                                             
CONECT    3    2    4    5                                                  
CONECT    4    3   12                                                       
CONECT    5    3   27                                                       
CONECT    6    2    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    2    4   13                                                  
CONECT   13   12   14   15   27                                             
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   16   26                                                  
CONECT   26   25                                                            
CONECT   27   13    5   28                                                  
CONECT   28   27                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₄O₇

Average Mass

398.4960 Da

Monoisotopic Mass

398.23045 Da

IUPAC Name

(1R,2R,5R,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}bicyclo[3.1.1]heptan-3-one

Traditional Name

(1R,2R,5R,6R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}bicyclo[3.1.1]heptan-3-one

CAS Registry Number

Not Available

SMILES

CC(C)=CCC[C@]1(C)[C@@H]2C[C@H]1[C@@](C)(O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(=O)C2

InChI Identifier

InChI=1S/C21H34O7/c1-11(2)6-5-7-20(3)12-8-14(20)21(4,15(23)9-12)28-19-18(26)17(25)16(24)13(10-22)27-19/h6,12-14,16-19,22,24-26H,5,7-10H2,1-4H3/t12-,13-,14-,16-,17+,18-,19+,20-,21-/m1/s1

InChI Key

VGDXREUUIOCSAE-JRWWIKKGSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	[email protected]	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	[email protected]	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500.033087685 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500.0, Methanol-d4, simulated)	[email protected]	Not Available	Not Available	2026-02-28	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125.0, Methanol-d4, simulated)	[email protected]	Not Available	Not Available	2026-02-28	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500.033087685, CD₃OD, simulated)	[email protected]	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Aspergillus nidulans LO8030 expressing bgtABCD		Not Available
Aspergillus nidulans LO8030 expressing bgtABCD		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. These are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl glycosides

Direct Parent

Fatty acyl glycosides of mono- and disaccharides

Alternative Parents

Substituents

Farsesane sesquiterpenoid
Bergamotane sesquiterpenoid
Sesquiterpenoid
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Fatty alcohol
Oxane
Monosaccharide
Cyclic ketone
Secondary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

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	1.27	ChemAxon
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	102.31 m³·mol⁻¹	ChemAxon
Polarizability	43.65 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yang W, Tian S, Du YF, Zeng XL, Liang JJ, Lan WJ, Li H: Genome Mining of the Marine-Derived Fungus Trichoderma erinaceum F1-1 Unearths Bergamotene-Type Sesquiterpenoids. J Nat Prod. 2024 Dec 27;87(12):2746-2756. doi: 10.1021/acs.jnatprod.4c00905. Epub 2024 Dec 2. [PubMed:39623525 ]
DOI: 10.1021/acs.jnatprod.4c00905
PMID: 39623525

Showing NP-Card for Bergamotene F (NP0333700)

MOL for NP0333700 (Bergamotene F)

3D MOL for NP0333700 (Bergamotene F)

3D SDF for NP0333700 (Bergamotene F)

3D-SDF for NP0333700 (Bergamotene F)

PDB for NP0333700 (Bergamotene F)

3D PDB for NP0333700 (Bergamotene F)

SMILES for NP0333700 (Bergamotene F)

INCHI for NP0333700 (Bergamotene F)

Structure for NP0333700 (Bergamotene F)

3D Structure for NP0333700 (Bergamotene F)