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Showing NP-Card for (-)-germacrene a (NP0156837)

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Record Information
Version2.0
Created at2022-09-02 14:06:33 UTC
Updated at2022-09-02 14:06:33 UTC
NP-MRD IDNP0156837
Secondary Accession NumbersNone
Natural Product Identification
Common Name(-)-germacrene a
Description(-)-Germacrene A 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. (-)-germacrene a is found in Acanthospermum australe, Acorus calamus, Aristolochia gigantea, Dictyopteris divaricata, Eunicea mammosa, Eunicea succinea, Frullania tamarisci, Linzia glabra, Magnolia sieboldii, Mentha piperita, Nasutitermes torresi, Ocimum basilicum, Piper cernuum, Protium heptaphyllum, Prumnopitys ferruginoides, Rugelia nudicaulis, Saussurea costus and Tilesia baccata. (-)-germacrene a was first documented in 2022 (PMID: 36035671). Based on a literature review a small amount of articles have been published on (-)-germacrene A (PMID: 35723427) (PMID: 35696915) (PMID: 35630799).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0156837 ((-)-germacrene a)


  Mrv1652309022216062D          

 15 15  0  0  1  0            999 V2000
    1.0326    3.2727    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
    2.4197    2.9295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.8998    0.0000 C   0  0  2  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
    1.8253    0.5269    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
    3.2124    0.1837    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
    1.4289   -1.0748    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
    1.0326    0.2981    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5394    0.9491    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
    0.6363    1.6710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  4  2  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  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  2  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
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3D MOL for NP0156837 ((-)-germacrene a)

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3D SDF for NP0156837 ((-)-germacrene a)

  Mrv1652309022216062D          

 15 15  0  0  1  0            999 V2000
    1.0326    3.2727    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
    2.4197    2.9295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.8998    0.0000 C   0  0  2  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
    1.8253    0.5269    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
    3.2124    0.1837    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
    1.4289   -1.0748    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
    1.0326    0.2981    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5394    0.9491    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
    0.6363    1.6710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  4  2  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  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  2  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>
NP0156837

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=C)[C@H]1CC\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/h6,9,15H,1,5,7-8,10-11H2,2-4H3/b13-6+,14-9+/t15-/m0/s1

> <INCHI_KEY>
XMRKUJJDDKYUHV-SDFJSLCBSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.357

> <EXACT_MASS>
204.187800773

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
25.58817078095862

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1E,5E,8S)-1,5-dimethyl-8-(prop-1-en-2-yl)cyclodeca-1,5-diene

> <ALOGPS_LOGP>
6.02

> <JCHEM_LOGP>
4.879526926666667

> <ALOGPS_LOGS>
-4.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
70.2829

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.46e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-germacrene A

> <JCHEM_VEBER_RULE>
1

$$$$

Download
3D-SDF for NP0156837 ((-)-germacrene a)
Download
PDB for NP0156837 ((-)-germacrene a)
HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       1.928   6.109   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.037   5.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.517   5.468   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   3.546   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.777   2.478   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.407   0.984   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       5.996   0.343   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.147  -1.579   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -2.006   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.558  -0.938   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.928   0.556   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.874   1.772   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.818   1.624   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.188   3.119   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                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    4                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

Download
3D PDB for NP0156837 ((-)-germacrene a)
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SMILES for NP0156837 ((-)-germacrene a)
CC(=C)[C@H]1CC\C(C)=C\CC\C(C)=C\C1
Download
INCHI for NP0156837 ((-)-germacrene a)
InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h6,9,15H,1,5,7-8,10-11H2,2-4H3/b13-6+,14-9+/t15-/m0/s1
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View in JSmol
Synonyms
ValueSource
(1E,5E,8S)-1,5-Dimethyl-8-(1-methylethenyl)-1,5-cyclodecadieneChEBI
(1E,5E,8S)-8-Isopropenyl-1,5-dimethylcyclodeca-1,5-dieneChEBI
(e,e)-Germacra-3,9,11-trieneChEBI
[S-(e,e)]-1,5-Dimethyl-8-(1-methylethenyl)-1,5-cyclodecadieneChEBI
Germacrene aChEBI
Chemical FormulaC15H24
Average Mass204.3570 Da
Monoisotopic Mass204.18780 Da
IUPAC Name(1E,5E,8S)-1,5-dimethyl-8-(prop-1-en-2-yl)cyclodeca-1,5-diene
Traditional Name(-)-germacrene A
CAS Registry NumberNot Available
SMILES
CC(=C)[C@H]1CC\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/h6,9,15H,1,5,7-8,10-11H2,2-4H3/b13-6+,14-9+/t15-/m0/s1
InChI KeyXMRKUJJDDKYUHV-SDFJSLCBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Acanthospermum australeLOTUS Database
Acorus calamusLOTUS Database
Aristolochia giganteaLOTUS Database
Dictyopteris divaricataLOTUS Database
Eunicea mammosaLOTUS Database
Eunicea succineaLOTUS Database
Frullania tamarisciLOTUS Database
Linzia glabraLOTUS Database
Magnolia sieboldiiLOTUS Database
Mentha piperitaLOTUS Database
Nasutitermes torresiLOTUS Database
Ocimum basilicumLOTUS Database
Piper cernuumLOTUS Database
Protium heptaphyllumLOTUS Database
Prumnopitys ferruginoidesLOTUS Database
Rugelia nudicaulisLOTUS Database
Saussurea costusLOTUS Database
Tilesia baccataLOTUS Database
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.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassSesquiterpenoids  
Direct ParentGermacrane sesquiterpenoids  
Alternative Parents
Substituents
  • Germacrane sesquiterpenoid
    • 

  • Branched unsaturated hydrocarbon
    • 

  • Cyclic olefin
    • 

  • Unsaturated aliphatic hydrocarbon
    • 

  • Unsaturated hydrocarbon
    • 

  • Olefin
    • 

  • Hydrocarbon
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP6.02ALOGPS
logP4.88ChemAxon
logS-4.4ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity70.28 m³·mol⁻¹ChemAxon
Polarizability25.59 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00011719  
Chemspider ID7827629  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9548706  
PDB IDNot Available
ChEBI ID36515  
Good Scents IDrw1562261  
References
General References
  1. Chen R, Liu Y, Chen S, Wang M, Zhu Y, Hu T, Wei Q, Yin X, Xie T: Protein Engineering of a Germacrene A Synthase From Lactuca sativa and Its Application in High Productivity of Germacrene A in Escherichia coli. Front Plant Sci. 2022 Aug 11;13:932966. doi: 10.3389/fpls.2022.932966.  eCollection 2022. [PubMed:36035671  ] 
  2. Shi Y, Dong T, Zeng B, Yao M, Wang Y, Xie Z, Xiao W, Yuan Y: Production of Plant Sesquiterpene Lactone Parthenolide in the Yeast Cell Factory. ACS Synth Biol. 2022 Jul 15;11(7):2473-2483. doi: 10.1021/acssynbio.2c00132. Epub  2022 Jun 20. [PubMed:35723427  ] 
  3. Hong CY, Tsao NW, Wang SY, Chu FH: Cloning and functional characterization of three sesquiterpene synthase genes from Chamaecyparis formosensis Matsumura. Plant Sci. 2022 Aug;321:111315. doi: 10.1016/j.plantsci.2022.111315. Epub 2022  May 18. [PubMed:35696915  ] 
  4. Xie DM, Zhang Q, Xin LK, Wang GK, Liu CB, Qin MJ: Cloning and Functional Characterization of Two Germacrene A Oxidases Isolated from Xanthium sibiricum. Molecules. 2022 May 22;27(10):3322. doi: 10.3390/molecules27103322. [PubMed:35630799  ] 
  5. LOTUS database [Link]