NP-MRD: Showing NP-Card for Oxybergamotene H (NP0341938)

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Record Information

Version

2.0

Created at

2024-11-05 12:45:15 UTC

Updated at

2025-06-12 01:07:58 UTC

NP-MRD ID

NP0341938

Natural Product DOI

https://doi.org/10.57994/3428

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Oxybergamotene H

Description

Based on a literature review very few articles have been published on Oxybergamotene H.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02022312562D          

 17 18  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
   -0.5362    1.5198    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
   -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
   -1.6569    3.3928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5136    4.2053    0.0000 O   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  2  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
    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
 11 12  1  0  0  0  0
  2 13  1  0  0  0  0
 13  4  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
  5 16  1  0  0  0  0
 16 17  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0341938

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@@H]2C[C@H](CC1=O)[C@@]2(C)CC\C=C(/C)CO

> <INCHI_IDENTIFIER>
InChI=1S/C15H24O2/c1-10(9-16)5-4-6-15(3)12-7-13(15)11(2)14(17)8-12/h5,11-13,16H,4,6-9H2,1-3H3/b10-5+/t11-,12+,13-,15+/m0/s1

> <INCHI_KEY>
UKAHUXKLRVYNDQ-AUSMANPISA-N

> <FORMULA>
C15H24O2

> <MOLECULAR_WEIGHT>
236.355

> <EXACT_MASS>
236.177630013

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
28.241860823685176

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,5R,6R)-6-[(3E)-5-hydroxy-4-methylpent-3-en-1-yl]-2,6-dimethylbicyclo[3.1.1]heptan-3-one

> <JCHEM_LOGP>
2.6629335026666663

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.64402351708654

> <JCHEM_PKA_STRONGEST_BASIC>
-2.079704113626345

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
70.11689999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5R,6R)-6-[(3E)-5-hydroxy-4-methylpent-3-en-1-yl]-2,6-dimethylbicyclo[3.1.1]heptan-3-one

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 02-FEB-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-FEB-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      -1.001   2.837   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.181   3.827   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.913   5.343   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.466   5.870   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.093   6.333   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -2.825   7.850   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.681  -1.003   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.221  -1.003   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.991  -2.337   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.991   0.330   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.531   0.330   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6   13                                             
CONECT    3    2    4    5                                                  
CONECT    4    3   13                                                       
CONECT    5    3   16                                                       
CONECT    6    2    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11                                                            
CONECT   13    2    4   14                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14    5   17                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₄O₂

Average Mass

236.3550 Da

Monoisotopic Mass

236.17763 Da

IUPAC Name

(1S,2S,5R,6R)-6-[(3E)-5-hydroxy-4-methylpent-3-en-1-yl]-2,6-dimethylbicyclo[3.1.1]heptan-3-one

Traditional Name

(1S,2S,5R,6R)-6-[(3E)-5-hydroxy-4-methylpent-3-en-1-yl]-2,6-dimethylbicyclo[3.1.1]heptan-3-one

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@@H]2C[C@H](CC1=O)[C@@]2(C)CC\C=C(/C)CO

InChI Identifier

InChI=1S/C15H24O2/c1-10(9-16)5-4-6-15(3)12-7-13(15)11(2)14(17)8-12/h5,11-13,16H,4,6-9H2,1-3H3/b10-5+/t11-,12+,13-,15+/m0/s1

InChI Key

UKAHUXKLRVYNDQ-AUSMANPISA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-11-05	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-11-05	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-11-05	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-11-05	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-11-05	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-11-05	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 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, 400, CD₃OD, simulated)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-11-05	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Aspergillus nidulans LO8030 expressing bgtABCD		Not Available

Chemical Taxonomy

Classification

Not classified

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	2.66	ChemAxon
pKa (Strongest Acidic)	16.64	ChemAxon
pKa (Strongest Basic)	-2.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	70.12 m³·mol⁻¹	ChemAxon
Polarizability	28.24 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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Oxybergamotene H (NP0341938)

MOL for NP0341938 (Oxybergamotene H)

3D MOL for NP0341938 (Oxybergamotene H)

3D SDF for NP0341938 (Oxybergamotene H)

3D-SDF for NP0341938 (Oxybergamotene H)

PDB for NP0341938 (Oxybergamotene H)

3D PDB for NP0341938 (Oxybergamotene H)

SMILES for NP0341938 (Oxybergamotene H)

INCHI for NP0341938 (Oxybergamotene H)

Structure for NP0341938 (Oxybergamotene H)

3D Structure for NP0341938 (Oxybergamotene H)