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Showing NP-Card for Germacrene A (NP0046863)

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Record Information
Version2.0
Created at2022-03-17 20:30:45 UTC
Updated at2022-03-17 20:30:45 UTC
NP-MRD IDNP0046863
Secondary Accession NumbersNone
Natural Product Identification
Common NameGermacrene A
DescriptionGermacrene 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 Aspergillus candidus, Dictyopteris divaricata, Eunicea succinea, Helminthosporium sativum, Magnolia sieboldii, Mentha piperita, Nasutitermes triodiae, Piper cernuum, Protium heptaphyllum, Prumnopitys ferruginoides, Saussurea costus, Scapania undulata, Tilesia baccata and Toona ciliata. Germacrene A is possibly neutral.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0046863 (Germacrene A)


  Mrv0541 02241221142D          

 15 15  0  0  1  0            999 V2000
    1.4289    1.8998    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
    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
    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  1  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
   -0.3545    0.6413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0418   -0.7316    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
    2.8161   -1.4180    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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  0  0  0  0
  1 13  1  0  0  0  0
  5 14  1  0  0  0  0
  1 15  1  0  0  0  0
M  END
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3D MOL for NP0046863 (Germacrene A)

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3D SDF for NP0046863 (Germacrene A)

  Mrv0541 02241221142D          

 15 15  0  0  1  0            999 V2000
    1.4289    1.8998    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
    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
    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  1  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
   -0.3545    0.6413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0418   -0.7316    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
    2.8161   -1.4180    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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  0  0  0  0
  1 13  1  0  0  0  0
  5 14  1  0  0  0  0
  1 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0046863

> <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-ZCGSDFCLSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.3511

> <EXACT_MASS>
204.187800768

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
25.933152460904736

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1Z,5Z,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

> <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

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0046863 (Germacrene A)
Download
PDB for NP0046863 (Germacrene A)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       2.667   3.546   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.777   2.479   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.407   0.984   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.517  -0.084   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.147  -1.579   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -2.006   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.558  -0.939   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.928   0.556   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.448   0.129   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.662   1.197   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.078  -1.366   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.818   1.624   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.188   3.119   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.257  -2.647   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.037   5.041   0.000  0.00  0.00           C+0
CONECT    1    2   13   15                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8   13                                                       
CONECT   13   12    1                                                       
CONECT   14    5                                                            
CONECT   15    1                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

Download
3D PDB for NP0046863 (Germacrene A)
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SMILES for NP0046863 (Germacrene A)
CC(=C)[C@H]1CC\C(C)=C/CC\C(C)=C/C1
Download
INCHI for NP0046863 (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
SynonymsNot Available
Chemical FormulaC15H24
Average Mass204.3511 Da
Monoisotopic Mass204.18780 Da
IUPAC Name(1Z,5Z,8S)-1,5-dimethyl-8-(prop-1-en-2-yl)cyclodeca-1,5-diene
Traditional Namegermacrene
CAS Registry Number28387-44-2
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-ZCGSDFCLSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Aspergillus candidusLOTUS Database
Dictyopteris divaricataLOTUS Database
Eunicea succineaLOTUS Database
Helminthosporium sativumFungi
Magnolia sieboldiiLOTUS Database
Mentha piperitaLOTUS Database
Nasutitermes triodiaeLOTUS Database
Ocimum basilicumFooDB
Piper cernuumLOTUS Database
Protium heptaphyllumLOTUS Database
Prumnopitys ferruginoidesLOTUS Database
Saussurea costusLOTUS Database
Scapania undulataLOTUS Database
Tilesia baccataLOTUS Database
Toona ciliataLOTUS 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 DescriptorsNot Available
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
Polarizability25.93 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 IDFDB006270  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGermacrene  
METLIN IDNot Available
PubChem Compound6440527  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available