NP-MRD: Showing NP-Card for sibirene (NP0288889)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-09 18:48:47 UTC

Updated at

2022-09-09 18:48:48 UTC

NP-MRD ID

NP0288889

Secondary Accession Numbers

None

Natural Product Identification

Common Name

sibirene

Description

Sibirene belongs to the class of organic compounds known as eudesmane, isoeudesmane or cycloeudesmane sesquiterpenoids. These are sesquiterpenoids with a structure based on the eudesmane skeleton. Thus, sibirene is considered to be an isoprenoid lipid molecule. sibirene is found in Abies sibirica, Hypericum perforatum, Larix gmelinii, Larix gmelinii, Larix kaempferi, Larix sibirica, Picea glehnii, Picea koraiensis, Picea orientalis, Pinus pumila, Pinus sibirica and Scapania undulata. Sibirene is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
   -1.3322    2.3676   -1.5184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3712    1.4700   -0.5501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9483    1.8554    0.7627 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7699    0.6421    1.2165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7469   -0.4572    1.4418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3261   -0.9466    0.0685 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5641   -1.5979   -0.5259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3024   -2.0598    0.2328 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0175   -1.5288    0.7333 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5054   -0.4566   -0.1990 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9605   -0.2382   -0.3232 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2147    0.8706   -1.3099 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5095    0.1343    1.0357 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6609    0.2544   -0.8738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8346    0.1176   -0.8243 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7180    3.3550   -1.3355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9242    2.1431   -2.4920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0825    1.9497    1.4672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5525    2.7577    0.7208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3482    0.8720    2.1263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4130    0.3784    0.3516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9112   -0.0758    2.0299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2906   -1.2994    1.9310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1112   -0.9248   -1.1925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2203   -1.9992    0.2966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2669   -2.4845   -1.1220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1192   -2.5155   -0.7644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6845   -2.8396    0.8922 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9944   -1.1964    1.7796 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7420   -2.3773    0.6732 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4719   -1.1815   -0.6731 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3322    1.0050   -1.3932 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7661    1.8172   -0.9928 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8125    0.6008   -2.3114 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2272    0.9635    0.8946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6888    0.4589    1.7059 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0594   -0.7315    1.4654 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0012    1.0290   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1262   -0.1316   -1.8759 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 13  1  0
 11 10  1  0
 10 14  2  0
 14 15  1  0
 15  2  1  0
  2  1  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  6
  6  8  1  0
  8  9  1  0
  9 10  1  0
  6 15  1  0
 12 32  1  0
 12 33  1  0
 12 34  1  0
 11 31  1  0
 13 35  1  0
 13 36  1  0
 13 37  1  0
 14 38  1  0
 15 39  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
  5 22  1  0
  5 23  1  0
  7 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
M  END


  Mrv1533004231522022D          

 15 16  0  0  0  0            999 V2000
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    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  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  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  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
  4 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0288889

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C1=CC2C(=C)CCCC2(C)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-11(2)13-7-9-15(4)8-5-6-12(3)14(15)10-13/h10-11,14H,3,5-9H2,1-2,4H3

> <INCHI_KEY>
ALUIZDJKPCNAGJ-UHFFFAOYSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
25.923687120985285

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4a-methyl-1-methylidene-7-(propan-2-yl)-1,2,3,4,4a,5,6,8a-octahydronaphthalene

> <ALOGPS_LOGP>
5.43

> <JCHEM_LOGP>
4.519309391666669

> <ALOGPS_LOGS>
-4.89

> <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>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.61e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sibirene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  -3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   15                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    6   13   14                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    4                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Value	Source
7-Isopropyl-4a-methyl-1-methylene-1,2,3,4,4a,5,6,8a-octahydronaphthalene	ChEBI

Chemical Formula

C₁₅H₂₄

Average Mass

204.3570 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

4a-methyl-1-methylidene-7-(propan-2-yl)-1,2,3,4,4a,5,6,8a-octahydronaphthalene

Traditional Name

sibirene

CAS Registry Number

Not Available

SMILES

CC(C)C1=CC2C(=C)CCCC2(C)CC1

InChI Identifier

InChI=1S/C15H24/c1-11(2)13-7-9-15(4)8-5-6-12(3)14(15)10-13/h10-11,14H,3,5-9H2,1-2,4H3

InChI Key

ALUIZDJKPCNAGJ-UHFFFAOYSA-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
Abies sibirica	LOTUS Database	35616633
Hypericum perforatum	LOTUS Database	35616633
Larix gmelini	LOTUS Database	35616633
Larix gmelinii var. olgensis	LOTUS Database	35616633
Larix kaempferi	LOTUS Database	35616633
Larix sibirica	LOTUS Database	35616633
Picea glehnii	LOTUS Database	35616633
Picea koraiensis	LOTUS Database	35616633
Picea orientalis	LOTUS Database	35616633
Pinus pumila	LOTUS Database	35616633
Pinus sibirica	LOTUS Database	35616633
Scapania undulata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as eudesmane, isoeudesmane or cycloeudesmane sesquiterpenoids. These are sesquiterpenoids with a structure based on the eudesmane skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Eudesmane, isoeudesmane or cycloeudesmane sesquiterpenoids

Alternative Parents

Substituents

Eudesmane, isoeudesmane or cycloeudesmane 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

sesquiterpene (CHEBI:49231 )
Eudesmane sesquiterpenoids (LMPR0103190005 )
a sesquiterpenoid (CPD-8731 )

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	5.43	ALOGPS
logP	4.52	ChemAxon
logS	-4.9	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	67.45 m³·mol⁻¹	ChemAxon
Polarizability	25.92 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

49231

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for sibirene (NP0288889)

MOL for NP0288889 (sibirene)

3D MOL for NP0288889 (sibirene)

3D SDF for NP0288889 (sibirene)

3D-SDF for NP0288889 (sibirene)

PDB for NP0288889 (sibirene)

3D PDB for NP0288889 (sibirene)

SMILES for NP0288889 (sibirene)

INCHI for NP0288889 (sibirene)

Structure for NP0288889 (sibirene)

3D Structure for NP0288889 (sibirene)