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Showing NP-Card for 2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol (NP0245417)

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Record Information
Version2.0
Created at2022-09-07 06:29:32 UTC
Updated at2022-09-07 06:29:32 UTC
NP-MRD IDNP0245417
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol
Description2,6-Dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol 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. 2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol is found in Peperomia heyneana and Sinularia gibberosa. 2,6-Dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0245417 (2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol)


  Mrv1533004171512402D          

 17 17  0  0  0  0            999 V2000
    0.0787    1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    2.9071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7792    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0492   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.8348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7314   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3488    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913    1.1921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.7243    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
  2  4  1  0  0  0  0
  4  5  1  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
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
  4 17  1  0  0  0  0
M  END
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3D MOL for NP0245417 (2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol)

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3D SDF for NP0245417 (2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol)

  Mrv1533004171512402D          

 17 17  0  0  0  0            999 V2000
    0.0787    1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    2.9071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7792    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0492   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.8348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7314   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3488    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913    1.1921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.7243    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
  2  4  1  0  0  0  0
  4  5  1  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
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
  4 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0245417

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=C)C1CCC(=C)C(O)CCC(=C)C(O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H24O2/c1-10(2)13-7-5-11(3)14(16)8-6-12(4)15(17)9-13/h13-17H,1,3-9H2,2H3

> <INCHI_KEY>
LFGFKWGAGHTKPW-UHFFFAOYSA-N

> <FORMULA>
C15H24O2

> <MOLECULAR_WEIGHT>
236.355

> <EXACT_MASS>
236.177630013

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
27.527336440625476

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol

> <ALOGPS_LOGP>
2.52

> <JCHEM_LOGP>
2.533772133333333

> <ALOGPS_LOGS>
-2.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.68533950251118

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.359595568087563

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9512257211697678

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
71.1689

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.10e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0245417 (2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol)
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PDB for NP0245417 (2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol)
HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       0.147   3.680   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.659   3.971   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.163   5.427   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   2.807   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.180   3.098   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.188   1.934   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.684   0.479   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.692  -0.685   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.171   0.188   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.180  -0.976   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.667  -1.267   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.155  -1.558   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.147  -0.394   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.365  -0.685   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.651   1.061   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -0.357   2.225   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.163   1.352   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    4                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

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3D PDB for NP0245417 (2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol)
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SMILES for NP0245417 (2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol)
CC(=C)C1CCC(=C)C(O)CCC(=C)C(O)C1
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INCHI for NP0245417 (2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol)
InChI=1S/C15H24O2/c1-10(2)13-7-5-11(3)14(16)8-6-12(4)15(17)9-13/h13-17H,1,3-9H2,2H3
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View in JSmol
SynonymsNot Available
Chemical FormulaC15H24O2
Average Mass236.3550 Da
Monoisotopic Mass236.17763 Da
IUPAC Name2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol
Traditional Name2,6-dimethylidene-9-(prop-1-en-2-yl)cyclodecane-1,5-diol
CAS Registry NumberNot Available
SMILES
CC(=C)C1CCC(=C)C(O)CCC(=C)C(O)C1
InChI Identifier
InChI=1S/C15H24O2/c1-10(2)13-7-5-11(3)14(16)8-6-12(4)15(17)9-13/h13-17H,1,3-9H2,2H3
InChI KeyLFGFKWGAGHTKPW-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Peperomia heyneanaLOTUS Database
Sinularia gibberosaLOTUS 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
    • 

  • Secondary alcohol
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • 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
logP2.52ALOGPS
logP2.53ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)18.36ChemAxon
pKa (Strongest Basic)-0.95ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity71.17 m³·mol⁻¹ChemAxon
Polarizability27.53 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73657170  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]