NP-MRD: Showing NP-Card for Germacrene B (NP0048538)

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Record Information

Version

2.0

Created at

2022-03-17 20:58:02 UTC

Updated at

2022-03-17 20:58:02 UTC

NP-MRD ID

NP0048538

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Germacrene B

Description

Germacrene B, also known as germacratriene, belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups. Thus, germacrene b is considered to be an isoprenoid lipid molecule. Germacrenes are a class of volatile organic hydrocarbons, specifically, sesquiterpenes. The essential oil of the red deadnettle (Lamium purpureum) is characterized by its high contents of germacrene D, as is Clausena anisata. Germacrene B is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Germacrene B is an earthy, spicy, and woody tasting compound. Outside of the human body, Germacrene B has been detected, but not quantified in, several different foods, such as citrus, common oregano, limes, and pepper (spice). This could make germacrene b a potential biomarker for the consumption of these foods. Two prominent molecules are germacrene A and germacrene D.Germacrene has five isomers. Germacrene B is found in Aspergillus candidus. Germacrenes are typically produced in a number of plant species for their antimicrobial and insecticidal properties, though they also play a role as insect pheromones.

Structure

MOL SDF PDB SMILES InChI

  Mrv0541 05061309122D          

 15 15  0  0  0  0            999 V2000
    0.0418   -0.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3545    0.6413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6271    2.7006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -1.4180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8253    0.5269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0234    1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4197   -0.0451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6363    1.6710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.0748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4381    0.8701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8345   -0.5028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2400    0.0693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.8998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2216   -0.8460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0326    0.2981    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  1  1  0  0  0  0
 12  2  1  0  0  0  0
 13  3  1  0  0  0  0
 13  6  2  0  0  0  0
 13  8  1  0  0  0  0
 14  4  1  0  0  0  0
 14  7  1  0  0  0  0
 14  9  2  0  0  0  0
 15 10  1  0  0  0  0
 15 11  1  0  0  0  0
 15 12  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0048538

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=C1CC\C(C)=C/CC\C(C)=C/C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h6,9H,5,7-8,10-11H2,1-4H3/b13-6-,14-9-

> <INCHI_KEY>
GXEGJTGWYVZSNR-OMQMMEOVSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.3511

> <EXACT_MASS>
204.187800768

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
26.13578962783003

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1Z,5Z)-1,5-dimethyl-8-(propan-2-ylidene)cyclodeca-1,5-diene

> <ALOGPS_LOGP>
5.87

> <JCHEM_LOGP>
4.777935431666666

> <ALOGPS_LOGS>
-3.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
71.0888

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.30e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1Z,4Z)-germacrene B

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       0.078  -1.366   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.662   1.197   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.037   5.041   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.257  -2.647   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.407   0.984   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.777   2.479   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.517  -0.084   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.188   3.119   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -2.006   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.818   1.624   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.558  -0.939   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.448   0.129   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   3.546   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.147  -1.579   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.928   0.556   0.000  0.00  0.00           C+0
CONECT    1   12                                                            
CONECT    2   12                                                            
CONECT    3   13                                                            
CONECT    4   14                                                            
CONECT    5    6    7                                                       
CONECT    6    5   13                                                       
CONECT    7    5   14                                                       
CONECT    8   10   13                                                       
CONECT    9   11   14                                                       
CONECT   10    8   15                                                       
CONECT   11    9   15                                                       
CONECT   12    1    2   15                                                  
CONECT   13    3    6    8                                                  
CONECT   14    4    7    9                                                  
CONECT   15   10   11   12                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
(1Z,5Z)-8-Isopropylidene-1,5-dimethylcyclodeca-1,5-diene	ChEBI
(1E,4E)-Germacra-1(10),4,7(11)-triene	HMDB
(1E,4E)-Germacrene b	HMDB
(1E,5E)-8-Isopropylidene-1,5-dimethylcyclodeca-1,5-diene	HMDB
(e,e)-Germacra-1(10),4,7(11)-triene	HMDB
(e,e)-Germacrene b	HMDB
Germacratriene	HMDB
trans,trans-Germacrene b	HMDB

Chemical Formula

C₁₅H₂₄

Average Mass

204.3511 Da

Monoisotopic Mass

204.18780 Da

IUPAC Name

(1Z,5Z)-1,5-dimethyl-8-(propan-2-ylidene)cyclodeca-1,5-diene

Traditional Name

(1Z,4Z)-germacrene B

CAS Registry Number

15423-57-1

SMILES

CC(C)=C1CC\C(C)=C/CC\C(C)=C/C1

InChI Identifier

InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h6,9H,5,7-8,10-11H2,1-4H3/b13-6-,14-9-

InChI Key

GXEGJTGWYVZSNR-OMQMMEOVSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Aspergillus candidus	LOTUS Database	35616633
Citrus aurantiifolia	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Origanum vulgare	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Piper nigrum L.	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Vitis	FooDB	PHYTOHUB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Germacrane sesquiterpenoids

Alternative Parents

Substituents

Germacrane sesquiterpenoid
Branched unsaturated hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

germacrene B (CHEBI:49655 )
Germacrane sesquiterpenoids (LMPR0103090011 )

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	5.87	ALOGPS
logP	4.78	ChemAxon
logS	-3.5	ALOGPS
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	71.09 m³·mol⁻¹	ChemAxon
Polarizability	26.14 Å³	ChemAxon
Number of Rings	1	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

HMDB0036575

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB015483

KNApSAcK ID

Not Available

Chemspider ID

4899018

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Germacrene

METLIN ID

Not Available

PubChem Compound

6370843

PDB ID

Not Available

ChEBI ID

49655

Good Scents ID

Not Available

References

General References

Showing NP-Card for Germacrene B (NP0048538)

MOL for NP0048538 (Germacrene B)

3D MOL for NP0048538 (Germacrene B)

3D SDF for NP0048538 (Germacrene B)

3D-SDF for NP0048538 (Germacrene B)

PDB for NP0048538 (Germacrene B)

3D PDB for NP0048538 (Germacrene B)

SMILES for NP0048538 (Germacrene B)

INCHI for NP0048538 (Germacrene B)

Structure for NP0048538 (Germacrene B)

3D Structure for NP0048538 (Germacrene B)