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Showing NP-Card for epomediol (NP0218574)

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Record Information
Version2.0
Created at2022-09-05 19:16:39 UTC
Updated at2022-09-05 19:16:39 UTC
NP-MRD IDNP0218574
Secondary Accession NumbersNone
Natural Product Identification
Common Nameepomediol
DescriptionExo,exo-1,8-Epoxy-p-menthane-2,6-diol, also known as 2,6-dihydroxycineol or exo,exo-form, belongs to the class of organic compounds known as oxanes. Oxanes are compounds containing an oxane (tetrahydropyran) ring, which is a six-member saturated aliphatic heterocycle with one oxygen atom and five carbon atoms. Exo,exo-1,8-Epoxy-p-menthane-2,6-diol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, exo,exo-1,8-Epoxy-p-menthane-2,6-diol has been detected, but not quantified in, herbs and spices. epomediol is found in Foeniculum vulgare. This could make exo,exo-1,8-epoxy-p-menthane-2,6-diol a potential biomarker for the consumption of these foods.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0218574 (epomediol)


  Mrv0541 05061312372D          

 13 14  0  0  0  0            999 V2000
    1.9302   -1.0045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6409   -0.0136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1682   -0.6402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1207   -2.0801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6726   -2.0684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9410   -1.7293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0159   -1.3418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5234   -1.3227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0775   -0.7143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8015   -0.9979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7277   -0.9433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2133   -1.5007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8384   -0.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
  9  6  1  0  0  0  0
 10  3  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
M  END
Download

3D MOL for NP0218574 (epomediol)

     RDKit          3D

 31 32  0  0  0  0  0  0  0  0999 V2000
    1.9603    1.4061    0.5631 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3970    0.0483    0.1539 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5297   -0.9124   -0.0353 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5036   -0.3193    1.1397 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8047   -0.3434    0.7536 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6643   -0.5476    1.9785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2705    0.9375    0.0855 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5876    1.9285    0.9730 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3090    1.3500   -0.9931 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6744    0.1902   -1.1591 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1242   -1.0526   -1.4700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9849   -1.4471   -0.2629 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3510   -1.4294   -0.6236 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1599    2.0254    1.0441 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3494    1.9480   -0.3000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7248    1.2656    1.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5246   -0.4014    0.0977 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5271   -1.7653    0.6425 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5800   -1.3195   -1.0868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4678    0.3277    2.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7214   -0.4750    1.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4085   -1.4527    2.5489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2289    0.6544   -0.4440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4095    2.4398    0.7426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2570    2.2574   -0.7703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7994    1.4616   -1.9922 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4009    0.3656   -1.9457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8227   -0.7733   -2.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5415   -1.8866   -1.7759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6979   -2.4372    0.1104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4780   -2.0431   -1.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  1
  5 12  1  0
 12 13  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  7  1  0
  7  8  1  0
 10  2  1  0
  7  5  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  6 20  1  0
  6 21  1  0
  6 22  1  0
 12 30  1  1
 13 31  1  0
 11 28  1  0
 11 29  1  0
 10 27  1  6
  9 25  1  0
  9 26  1  0
  7 23  1  6
  8 24  1  0
M  END
Download

3D SDF for NP0218574 (epomediol)


  Mrv0541 05061312372D          

 13 14  0  0  0  0            999 V2000
    1.9302   -1.0045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6409   -0.0136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1682   -0.6402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1207   -2.0801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6726   -2.0684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9410   -1.7293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0159   -1.3418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5234   -1.3227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0775   -0.7143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8015   -0.9979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7277   -0.9433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2133   -1.5007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8384   -0.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
  9  6  1  0  0  0  0
 10  3  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0218574

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)OC2(C)C(O)CC1CC2O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O3/c1-9(2)6-4-7(11)10(3,13-9)8(12)5-6/h6-8,11-12H,4-5H2,1-3H3

> <INCHI_KEY>
JSNQSLSBBZFGBM-UHFFFAOYSA-N

> <FORMULA>
C10H18O3

> <MOLECULAR_WEIGHT>
186.2481

> <EXACT_MASS>
186.125594442

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
20.097629628089464

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,3,3-trimethyl-2-oxabicyclo[2.2.2]octane-6,7-diol

> <ALOGPS_LOGP>
0.68

> <JCHEM_LOGP>
0.19861239233333336

> <ALOGPS_LOGS>
-0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.304546290772333

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.606570692183787

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2766154591353853

> <JCHEM_POLAR_SURFACE_AREA>
49.69

> <JCHEM_REFRACTIVITY>
48.58389999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.92e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
epomediol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0218574 (epomediol)

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PDB for NP0218574 (epomediol)
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       3.603  -1.875   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.063  -0.025   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.314  -1.195   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.225  -3.883   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.122  -3.861   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.757  -3.228   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.030  -2.505   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.844  -2.469   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.011  -1.333   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.496  -1.863   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.358  -1.761   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.132  -2.801   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.565  -0.228   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4    6    7                                                       
CONECT    5    6    8                                                       
CONECT    6    4    5    9                                                  
CONECT    7    4   10   11                                                  
CONECT    8    5   10   12                                                  
CONECT    9    1    2    6   13                                             
CONECT   10    3    7    8   13                                             
CONECT   11    7                                                            
CONECT   12    8                                                            
CONECT   13    9   10                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

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3D PDB for NP0218574 (epomediol)
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SMILES for NP0218574 (epomediol)
CC1(C)OC2(C)C(O)CC1CC2O
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INCHI for NP0218574 (epomediol)
InChI=1S/C10H18O3/c1-9(2)6-4-7(11)10(3,13-9)8(12)5-6/h6-8,11-12H,4-5H2,1-3H3
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View in JSmol
Synonyms
ValueSource
2,6-DihydroxycineolKegg
1,8-Epoxy-p-menthane-2,6-diolHMDB
exo,exo-FormHMDB
ClesidrenHMDB
1,8-Epoxy-1-methyl-4-isopropylcyclohexane-2,6-diolHMDB
Chemical FormulaC10H18O3
Average Mass186.2481 Da
Monoisotopic Mass186.12559 Da
IUPAC Name1,3,3-trimethyl-2-oxabicyclo[2.2.2]octane-6,7-diol
Traditional Nameepomediol
CAS Registry NumberNot Available
SMILES
CC1(C)OC2(C)C(O)CC1CC2O
InChI Identifier
InChI=1S/C10H18O3/c1-9(2)6-4-7(11)10(3,13-9)8(12)5-6/h6-8,11-12H,4-5H2,1-3H3
InChI KeyJSNQSLSBBZFGBM-UHFFFAOYSA-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
Foeniculum vulgareLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxanes. Oxanes are compounds containing an oxane (tetrahydropyran) ring, which is a six-member saturated aliphatic heterocycle with one oxygen atom and five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassOxanes  
Sub ClassNot Available
Direct ParentOxanes  
Alternative Parents
Substituents
  • Oxane
    • 

  • Cyclic alcohol
    • 

  • Secondary alcohol
    • 

  • Oxacycle
    • 

  • Ether
    • 

  • Dialkyl ether
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic 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
logP0.68ALOGPS
logP0.2ChemAxon
logS-0.37ALOGPS
pKa (Strongest Acidic)13.61ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.69 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity48.58 m³·mol⁻¹ChemAxon
Polarizability20.1 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0041376  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021306  
KNApSAcK IDNot Available
Chemspider ID102967  
KEGG Compound IDC17620  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound115056  
PDB IDNot Available
ChEBI ID81225  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]