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Showing NP-Card for (1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol (NP0255093)

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Record Information
Version2.0
Created at2022-09-07 19:27:39 UTC
Updated at2022-09-07 19:27:39 UTC
NP-MRD IDNP0255093
Secondary Accession NumbersNone
Natural Product Identification
Common Name(1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol
Description(-)-Trans-Pinocarveol, also known as L-pinocarveol, belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other (-)-trans-Pinocarveol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (-)-trans-Pinocarveol is found, on average, in the highest concentration within a few different foods, such as hyssops, rosemaries, and cumins (-)-trans-Pinocarveol has also been detected, but not quantified in, a few different foods, such as common sages, pepper (spice), and sweet bay. (1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol is found in Anthemis aciphylla, Artemisia annua, Artemisia herba-alba, Cedrus libani, Cistus creticus, Cyperus rotundus, Pinus koraiensis, Pinus sylvestris, Rhodiola rosea, Teucrium leucocladum and Teucrium polium. This could make (-)-trans-pinocarveol a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0255093 ((1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol)


  Mrv1652309272007422D          

 11 12  0  0  0  0            999 V2000
 9999.073710001.0103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.544010000.0927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0670 9999.8199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.495910000.6474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4959 9998.9937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.067710000.6448    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.353210000.2323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3532 9999.4072    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.0677 9998.9948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7822 9999.4072    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.782210000.2323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  7  1  0  0  0  0
  6 11  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11  4  2  0  0  0  0
 10  5  1  1  0  0  0
  7  2  1  0  0  0  0
  1  7  1  0  0  0  0
  8  3  1  1  0  0  0
  6  3  1  1  0  0  0
M  END
Download

3D MOL for NP0255093 ((1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol)

     RDKit          3D

 27 28  0  0  0  0  0  0  0  0999 V2000
    1.6096    1.3949    1.6246 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1240    0.5667    0.7308 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6417    0.5573   -0.6669 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8729   -0.0834   -0.7286 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6248   -0.0391   -1.5959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3879   -0.9023   -0.8843 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2774   -1.6487    0.2499 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0476   -0.3828    1.0842 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1355   -0.1109    0.1804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3684   -0.8501    0.6335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3755    1.3107   -0.1848 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2397    1.4068    2.6368 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3977    2.0837    1.3489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8175    1.6298   -0.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9862   -0.6474   -1.5145 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0838   -0.6731   -2.3858 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0512    0.7870   -2.0789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0024   -1.4804   -1.5642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3675   -2.4896    0.5636 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3198   -1.8628    0.0228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1609   -0.5464    2.1346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1522   -1.4169    1.5700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6722   -1.5480   -0.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2062   -0.1199    0.8197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4282    1.8760   -0.1308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7411    1.4189   -1.2462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0957    1.7700    0.5125 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9 11  1  0
  9  6  1  0
  6  7  1  0
  7  8  1  0
  8  2  1  0
  2  1  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  8  9  1  0
  5  6  1  0
 10 22  1  0
 10 23  1  0
 10 24  1  0
 11 25  1  0
 11 26  1  0
 11 27  1  0
  6 18  1  6
  7 19  1  0
  7 20  1  0
  8 21  1  1
  1 12  1  0
  1 13  1  0
  3 14  1  6
  4 15  1  0
  5 16  1  0
  5 17  1  0
M  END
Download

3D SDF for NP0255093 ((1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol)


  Mrv1652309272007422D          

 11 12  0  0  0  0            999 V2000
 9999.073710001.0103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.544010000.0927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0670 9999.8199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.495910000.6474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4959 9998.9937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.067710000.6448    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.353210000.2323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3532 9999.4072    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.0677 9998.9948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7822 9999.4072    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.782210000.2323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  7  1  0  0  0  0
  6 11  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11  4  2  0  0  0  0
 10  5  1  1  0  0  0
  7  2  1  0  0  0  0
  1  7  1  0  0  0  0
  8  3  1  1  0  0  0
  6  3  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0255093

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)[C@@H]2C[C@H]1C(=C)[C@@H](O)C2

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O/c1-6-8-4-7(5-9(6)11)10(8,2)3/h7-9,11H,1,4-5H2,2-3H3/t7-,8+,9+/m1/s1

> <INCHI_KEY>
LCYXQUJDODZYIJ-VGMNWLOBSA-N

> <FORMULA>
C10H16O

> <MOLECULAR_WEIGHT>
152.2334

> <EXACT_MASS>
152.120115134

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
17.88230893843388

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3S,5R)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol

> <ALOGPS_LOGP>
2.24

> <JCHEM_LOGP>
1.628784049666666

> <ALOGPS_LOGS>
-1.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.937417626307106

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5139735302532715

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
45.1653

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.76e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3S,5R)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0255093 ((1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol)

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PDB for NP0255093 ((1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol)
HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0    8664.9388668.553   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8663.9498666.840   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8666.7928666.330   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8669.4598667.875   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8669.4598664.788   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0    8666.7938667.870   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8665.4598667.100   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8665.4598665.560   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8666.7938664.790   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8668.1278665.560   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8668.1278667.100   0.000  0.00  0.00           C+0
CONECT    1    7                                                            
CONECT    2    7                                                            
CONECT    3    8    6                                                       
CONECT    4   11                                                            
CONECT    5   10                                                            
CONECT    6    7   11    3                                                  
CONECT    7    6    8    2    1                                             
CONECT    8    7    9    3                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11    5                                                  
CONECT   11    6   10    4                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END

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3D PDB for NP0255093 ((1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol)
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SMILES for NP0255093 ((1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol)
CC1(C)[C@@H]2C[C@H]1C(=C)[C@@H](O)C2
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INCHI for NP0255093 ((1r,3s,5r)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol)
InChI=1S/C10H16O/c1-6-8-4-7(5-9(6)11)10(8,2)3/h7-9,11H,1,4-5H2,2-3H3/t7-,8+,9+/m1/s1
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View in JSmol
Synonyms
ValueSource
(-)-trans-2(10)-Pinen-3-olHMDB
(1S)-(-)-trans-PinocarveolHMDB
(1S,3R,5S)-(-)-2(10)-Pinen-3-olHMDB
L-PinocarveolHMDB
L-trans-PinocarveolHMDB
trans-(-)-PinocarveolHMDB
10-Pinen-3-olPhytoBank
2(10)-Pinen-3-olPhytoBank
6,6-Dimethyl-2-methylenebicyclo[3.1.1]heptan-3-olPhytoBank
PinocarveolePhytoBank
trans-2(10)-Pinen-3-olPhytoBank
(±)-trans-PinocarveolPhytoBank
Chemical FormulaC10H16O
Average Mass152.2334 Da
Monoisotopic Mass152.12012 Da
IUPAC Name(1R,3S,5R)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol
Traditional Name(1R,3S,5R)-6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptan-3-ol
CAS Registry NumberNot Available
SMILES
CC1(C)[C@@H]2C[C@H]1C(=C)[C@@H](O)C2
InChI Identifier
InChI=1S/C10H16O/c1-6-8-4-7(5-9(6)11)10(8,2)3/h7-9,11H,1,4-5H2,2-3H3/t7-,8+,9+/m1/s1
InChI KeyLCYXQUJDODZYIJ-VGMNWLOBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anthemis aciphyllaLOTUS Database
Artemisia annuaLOTUS Database
Artemisia herba-albaLOTUS Database
Cedrus libaniLOTUS Database
Cistus creticusLOTUS Database
Cyperus rotundusLOTUS Database
Pinus koraiensisLOTUS Database
Pinus sylvestrisLOTUS Database
Rhodiola roseaLOTUS Database
Teucrium leucocladumLOTUS Database
Teucrium poliumLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassMonoterpenoids  
Direct ParentBicyclic monoterpenoids  
Alternative Parents
Substituents
  • Pinane monoterpenoid
    • 

  • Bicyclic monoterpenoid
    • 

  • Cyclic alcohol
    • 

  • Secondary alcohol
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic 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
logP2.24ALOGPS
logP1.63ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)17.94ChemAxon
pKa (Strongest Basic)-1.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity45.17 m³·mol⁻¹ChemAxon
Polarizability17.88 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0036128  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB014367  
KNApSAcK IDC00011040  
Chemspider ID1013323  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1201530  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]