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Showing NP-Card for [10]-Gingerdiol (NP0049315)

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Record Information
Version2.0
Created at2022-03-17 21:10:31 UTC
Updated at2022-03-17 21:10:31 UTC
NP-MRD IDNP0049315
Secondary Accession NumbersNone
Natural Product Identification
Common Name[10]-Gingerdiol
Description[10]-Gingerdiol belongs to the class of organic compounds known as gingerdiols. Gingerdiols are compounds containing a gingerdiol moiety, which is structurally characterized by a 4-hydroxy-3-methoxyphenyl group substituted at the C6 carbon atom by an alkane-2,4-diol. [10]-Gingerdiol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, [10]-Gingerdiol has been detected, but not quantified in, gingers. This could make [10]-gingerdiol a potential biomarker for the consumption of these foods.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0049315 ([10]-Gingerdiol)


  Mrv1652310081711472D          

 25 25  0  0  0  0            999 V2000
  -10.0026    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5737    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  2  0  0  0  0
 17 11  1  0  0  0  0
 17 12  1  0  0  0  0
 17 15  2  0  0  0  0
 18 10  1  0  0  0  0
 18 16  1  0  0  0  0
 19 13  1  0  0  0  0
 19 16  1  0  0  0  0
 20 14  1  0  0  0  0
 21 15  1  0  0  0  0
 21 20  2  0  0  0  0
 22 18  1  0  0  0  0
 23 19  1  0  0  0  0
 24 20  1  0  0  0  0
 25  2  1  0  0  0  0
 25 21  1  0  0  0  0
M  END
Download

3D MOL for NP0049315 ([10]-Gingerdiol)

Download
3D SDF for NP0049315 ([10]-Gingerdiol)

  Mrv1652310081711472D          

 25 25  0  0  0  0            999 V2000
  -10.0026    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5737    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  2  0  0  0  0
 17 11  1  0  0  0  0
 17 12  1  0  0  0  0
 17 15  2  0  0  0  0
 18 10  1  0  0  0  0
 18 16  1  0  0  0  0
 19 13  1  0  0  0  0
 19 16  1  0  0  0  0
 20 14  1  0  0  0  0
 21 15  1  0  0  0  0
 21 20  2  0  0  0  0
 22 18  1  0  0  0  0
 23 19  1  0  0  0  0
 24 20  1  0  0  0  0
 25  2  1  0  0  0  0
 25 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049315

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCC(O)CC(O)CCC1=CC(OC)=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C21H36O4/c1-3-4-5-6-7-8-9-10-18(22)16-19(23)13-11-17-12-14-20(24)21(15-17)25-2/h12,14-15,18-19,22-24H,3-11,13,16H2,1-2H3

> <INCHI_KEY>
LGSIUDXMEDKEPY-UHFFFAOYSA-N

> <FORMULA>
C21H36O4

> <MOLECULAR_WEIGHT>
352.5081

> <EXACT_MASS>
352.26135964

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
43.20779594554172

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(4-hydroxy-3-methoxyphenyl)tetradecane-3,5-diol

> <ALOGPS_LOGP>
5.16

> <JCHEM_LOGP>
4.958592203

> <ALOGPS_LOGS>
-4.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.871448004426892

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.277057619232806

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7208399833925805

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
102.65169999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.85e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(4-hydroxy-3-methoxyphenyl)tetradecane-3,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0049315 ([10]-Gingerdiol)
Download
PDB for NP0049315 ([10]-Gingerdiol)
HEADER    PROTEIN                                 08-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-OCT-17         0                                  
HETATM    1  C   UNK     0     -18.672   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -17.338   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -16.004   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -14.670   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -13.337   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -12.003   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -10.669   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -9.336   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -6.668   3.850   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2   25                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   18                                                       
CONECT   11   13   17                                                       
CONECT   12   14   17                                                       
CONECT   13   11   19                                                       
CONECT   14   12   20                                                       
CONECT   15   17   21                                                       
CONECT   16   18   19                                                       
CONECT   17   11   12   15                                                  
CONECT   18   10   16   22                                                  
CONECT   19   13   16   23                                                  
CONECT   20   14   21   24                                                  
CONECT   21   15   20   25                                                  
CONECT   22   18                                                            
CONECT   23   19                                                            
CONECT   24   20                                                            
CONECT   25    2   21                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   50    0
END

Download
3D PDB for NP0049315 ([10]-Gingerdiol)
Download
SMILES for NP0049315 ([10]-Gingerdiol)
CCCCCCCCCC(O)CC(O)CCC1=CC(OC)=C(O)C=C1
Download
INCHI for NP0049315 ([10]-Gingerdiol)
InChI=1S/C21H36O4/c1-3-4-5-6-7-8-9-10-18(22)16-19(23)13-11-17-12-14-20(24)21(15-17)25-2/h12,14-15,18-19,22-24H,3-11,13,16H2,1-2H3
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View in JSmol
SynonymsNot Available
Chemical FormulaC21H36O4
Average Mass352.5081 Da
Monoisotopic Mass352.26136 Da
IUPAC Name1-(4-hydroxy-3-methoxyphenyl)tetradecane-3,5-diol
Traditional Name1-(4-hydroxy-3-methoxyphenyl)tetradecane-3,5-diol
CAS Registry Number53254-77-6
SMILES
CCCCCCCCCC(O)CC(O)CCC1=CC(OC)=C(O)C=C1
InChI Identifier
InChI=1S/C21H36O4/c1-3-4-5-6-7-8-9-10-18(22)16-19(23)13-11-17-12-14-20(24)21(15-17)25-2/h12,14-15,18-19,22-24H,3-11,13,16H2,1-2H3
InChI KeyLGSIUDXMEDKEPY-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Zingiber officinaleFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gingerdiols. Gingerdiols are compounds containing a gingerdiol moiety, which is structurally characterized by a 4-hydroxy-3-methoxyphenyl group substituted at the C6 carbon atom by an alkane-2,4-diol.
KingdomOrganic compounds  
Super ClassBenzenoids  
ClassPhenols  
Sub ClassMethoxyphenols  
Direct ParentGingerdiols  
Alternative Parents
Substituents
  • Gingerdiol
    • 

  • Fatty alcohol
    • 

  • Phenoxy compound
    • 

  • Anisole
    • 

  • Methoxybenzene
    • 

  • Phenol ether
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Alkyl aryl ether
    • 

  • Monocyclic benzene moiety
    • 

  • Fatty acyl
    • 

  • Secondary alcohol
    • 

  • Ether
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic 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
logP5.16ALOGPS
logP4.96ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)10.28ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.92 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity102.65 m³·mol⁻¹ChemAxon
Polarizability43.21 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0164513  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB018650  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5317590  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available