NP-MRD: Showing NP-Card for (1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene (NP0215302)

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Record Information

Version

2.0

Created at

2022-09-05 14:52:55 UTC

Updated at

2022-09-05 14:52:56 UTC

NP-MRD ID

NP0215302

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

Description

Isobicyclogermacrene belongs to the class of organic compounds known as bicyclogermacrane and isolepidozane sesquiterpenoids. These are sesquiterpenoids with a structure based either on the bicyclogermacrane (3,7,11,11-tetramethylbicyclo[8.1.0]Undecane, 9CI) skeleton or the isolepidozane skeleton. (1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene is found in Scapania undulata. (1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene was first documented in 2016 (PMID: 27319120). Based on a literature review very few articles have been published on Isobicyclogermacrene.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
   -0.5791    3.6802   -0.8156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3726    2.2423   -0.3390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3855    1.5646    0.1550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2882    0.1979    0.6316 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8344   -0.8184   -0.2940 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2014   -1.6776    0.4185 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4569   -1.7255   -0.3809 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6111   -0.9759    0.1300 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9414   -1.7329    0.0495 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6788    0.2268    0.6304 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5870    1.2117    0.8449 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9587    1.6440   -0.4437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2688   -0.8599    0.0303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2353   -0.3154   -1.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8699   -1.8848    0.9211 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2071    3.9162   -1.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6000    3.8315   -1.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4068    4.2910    0.1005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3531    2.0737    0.2036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2152   -0.0088    1.7357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6195   -0.7084   -1.3656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2944   -2.6999    0.4854 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3366   -1.3996    1.4826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1923   -1.4542   -1.4475 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6978   -2.8265   -0.4892 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7865   -1.0504    0.0905 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9594   -2.2246   -0.9456 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0173   -2.4559    0.8695 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6795    0.6246    0.9624 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8813    0.8872    1.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0135    2.1690    1.3125 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0660    0.8885   -1.2684 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6529    2.4693   -0.8361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6525   -1.2139   -1.5362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1063    0.1889   -0.5469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7244    0.2857   -1.7722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0585   -2.8117    0.3613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8381   -1.5020    1.3212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2228   -2.0467    1.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8 10  2  0
 10 11  1  0
 11 12  1  0
 12  2  1  0
  2  1  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  5 13  1  0
 13 14  1  0
 13 15  1  0
  7  8  1  0
 13  4  1  0
  9 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  1
  5 21  1  6
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  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
M  END


  Mrv1652309052216522D          

 15 16  0  0  1  0            999 V2000
    1.6172   -0.8183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5942    0.0064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8027    0.2394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2994    0.8930    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2763    1.7177    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7425    2.3984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5197    2.6751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0230    2.0215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5569    1.3408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8144    1.7885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8375    0.9639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3714    0.2832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4263    1.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1151    1.7396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0887    0.7935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  2 12  1  0  0  0  0
  5 13  1  0  0  0  0
  4 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0215302

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C1=C/CC\C(C)=C/[C@@H]2[C@@H](CC1)C2(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-11-6-5-7-12(2)10-14-13(9-8-11)15(14,3)4/h6,10,13-14H,5,7-9H2,1-4H3/b11-6+,12-10-/t13-,14-/m1/s1

> <INCHI_KEY>
VPDZRSSKICPUEY-ITVLWJPGSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
25.965305682201723

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2Z,6E,10R)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

> <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>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2Z,6E,10R)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       3.019  -1.527   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.976   0.012   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.498   0.447   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.559   1.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.516   3.206   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.386   4.477   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.837   4.994   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.776   3.773   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.906   2.503   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.254   3.339   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.297   1.799   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.427   0.529   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.796   2.399   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.081   3.247   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.032   1.481   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   13                                                  
CONECT    5    4    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    2                                                       
CONECT   13    5    4   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

Not Available

Chemical Formula

C₁₅H₂₄

Average Mass

204.3570 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

(1R,2Z,6E,10R)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

Traditional Name

(1R,2Z,6E,10R)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

CAS Registry Number

Not Available

SMILES

C\C1=C/CC\C(C)=C/[C@@H]2[C@@H](CC1)C2(C)C

InChI Identifier

InChI=1S/C15H24/c1-11-6-5-7-12(2)10-14-13(9-8-11)15(14,3)4/h6,10,13-14H,5,7-9H2,1-4H3/b11-6+,12-10-/t13-,14-/m1/s1

InChI Key

VPDZRSSKICPUEY-ITVLWJPGSA-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
Scapania undulata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bicyclogermacrane and isolepidozane sesquiterpenoids. These are sesquiterpenoids with a structure based either on the bicyclogermacrane (3,7,11,11-tetramethylbicyclo[8.1.0]Undecane, 9CI) skeleton or the isolepidozane skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Bicyclogermacrane and isolepidozane sesquiterpenoids

Alternative Parents

Substituents

Bicyclogermacrane sesquiterpenoid
Branched unsaturated hydrocarbon
Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	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	0	ChemAxon
Refractivity	68.52 m³·mol⁻¹	ChemAxon
Polarizability	25.97 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

C00037322

Chemspider ID

9162581

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16055278

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lin YS, Su JH, Lo CL, Huang CY, Sheu JH: Isobicyclogermacrene-type Sesquiterpenoids from the Soft Coral Sinularia lochmodes. Nat Prod Commun. 2016 May;11(5):577-8. [PubMed:27319120 ]
LOTUS database [Link]

Showing NP-Card for (1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene (NP0215302)

MOL for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

3D MOL for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

3D SDF for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

3D-SDF for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

PDB for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

3D PDB for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

SMILES for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

INCHI for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

Structure for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)

3D Structure for NP0215302 ((1r,2z,6e,10r)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene)