Np mrd loader

Showing NP-Card for Glyceollidin II (NP0048937)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-03-17 21:04:32 UTC
Updated at2022-03-17 21:04:33 UTC
NP-MRD IDNP0048937
Secondary Accession NumbersNone
Natural Product Identification
Common NameGlyceollidin II
DescriptionGlyceollidin II, also known as glyceocarpin, belongs to the class of organic compounds known as pterocarpans. These are benzo-pyrano-furano-benzene compounds, containing the 6H-[1]benzofuro[3,2-c]chromene skeleton. They are derivatives of isoflavonoids. Glyceollidin II is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, glyceollidin II has been detected, but not quantified in, a few different foods, such as fats and oils, pulses, and soy beans. Glyceollidin II is found in Taxus fuana and Taxus yunnanensis. This could make glyceollidin II a potential biomarker for the consumption of these foods.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0048937 (Glyceollidin II)


  Mrv0541 05061310052D          

 25 28  0  0  0  0            999 V2000
    7.8559   -3.9480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6613   -4.7321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5796   -3.3055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7559   -3.3526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5275   -1.5272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2608   -1.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4796   -2.7100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1823   -2.7972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2216   -1.2363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1217   -0.6408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0322   -3.9952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3033   -2.6629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4883   -2.3512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0270   -2.0203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9548   -1.5951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6743   -1.9260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3980   -1.2834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9156   -2.4191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2033   -2.0674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7507   -1.3777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2450   -2.7293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4979   -1.8789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2284   -0.7391    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9453   -0.5937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6872   -2.7111    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  2  0  0  0  0
 11  1  1  0  0  0  0
 11  2  1  0  0  0  0
 11  3  2  0  0  0  0
 12  4  1  0  0  0  0
 12  7  2  0  0  0  0
 13  5  1  0  0  0  0
 13  8  2  0  0  0  0
 14  7  1  0  0  0  0
 15  6  1  0  0  0  0
 16  9  2  0  0  0  0
 16 12  1  0  0  0  0
 17  9  1  0  0  0  0
 17 14  2  0  0  0  0
 18  8  1  0  0  0  0
 18 15  2  0  0  0  0
 19 14  1  0  0  0  0
 20 10  1  0  0  0  0
 20 15  1  0  0  0  0
 20 19  1  0  0  0  0
 21 13  1  0  0  0  0
 22 16  1  0  0  0  0
 23 20  1  0  0  0  0
 24 10  1  0  0  0  0
 24 17  1  0  0  0  0
 25 18  1  0  0  0  0
 25 19  1  0  0  0  0
M  END
Download

3D MOL for NP0048937 (Glyceollidin II)

Download
3D SDF for NP0048937 (Glyceollidin II)

  Mrv0541 05061310052D          

 25 28  0  0  0  0            999 V2000
    7.8559   -3.9480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6613   -4.7321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5796   -3.3055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7559   -3.3526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5275   -1.5272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2608   -1.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4796   -2.7100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1823   -2.7972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2216   -1.2363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1217   -0.6408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0322   -3.9952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3033   -2.6629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4883   -2.3512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0270   -2.0203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9548   -1.5951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6743   -1.9260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3980   -1.2834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9156   -2.4191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2033   -2.0674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7507   -1.3777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2450   -2.7293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4979   -1.8789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2284   -0.7391    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9453   -0.5937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6872   -2.7111    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  2  0  0  0  0
 11  1  1  0  0  0  0
 11  2  1  0  0  0  0
 11  3  2  0  0  0  0
 12  4  1  0  0  0  0
 12  7  2  0  0  0  0
 13  5  1  0  0  0  0
 13  8  2  0  0  0  0
 14  7  1  0  0  0  0
 15  6  1  0  0  0  0
 16  9  2  0  0  0  0
 16 12  1  0  0  0  0
 17  9  1  0  0  0  0
 17 14  2  0  0  0  0
 18  8  1  0  0  0  0
 18 15  2  0  0  0  0
 19 14  1  0  0  0  0
 20 10  1  0  0  0  0
 20 15  1  0  0  0  0
 20 19  1  0  0  0  0
 21 13  1  0  0  0  0
 22 16  1  0  0  0  0
 23 20  1  0  0  0  0
 24 10  1  0  0  0  0
 24 17  1  0  0  0  0
 25 18  1  0  0  0  0
 25 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048937

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC1=CC2=C(OCC3(O)C2OC2=C3C=CC(O)=C2)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H20O5/c1-11(2)3-4-12-7-14-17(9-16(12)22)24-10-20(23)15-6-5-13(21)8-18(15)25-19(14)20/h3,5-9,19,21-23H,4,10H2,1-2H3

> <INCHI_KEY>
TUXXPRXOVFCNPC-UHFFFAOYSA-N

> <FORMULA>
C20H20O5

> <MOLECULAR_WEIGHT>
340.3698

> <EXACT_MASS>
340.13107375

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
36.59704337741472

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-(3-methylbut-2-en-1-yl)-8,17-dioxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-2(7),3,5,11(16),12,14-hexaene-5,10,14-triol

> <ALOGPS_LOGP>
2.83

> <JCHEM_LOGP>
3.4367159576666664

> <ALOGPS_LOGS>
-3.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.615435483540304

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.994990711471155

> <JCHEM_PKA_STRONGEST_BASIC>
-4.093993926428898

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
93.9095

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.72e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-(3-methylbut-2-en-1-yl)-8,17-dioxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-2(7),3,5,11(16),12,14-hexaene-5,10,14-triol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0048937 (Glyceollidin II)
Download
PDB for NP0048937 (Glyceollidin II)
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      14.664  -7.370   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.434  -8.833   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.282  -6.170   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.744  -6.258   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.985  -2.851   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.353  -2.145   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.362  -5.059   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.207  -5.221   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.747  -2.308   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.827  -1.196   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.127  -7.458   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.899  -4.971   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.911  -4.389   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.517  -3.771   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.649  -2.978   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.592  -3.595   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.210  -2.396   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.576  -4.516   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.979  -3.859   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.135  -2.572   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.457  -5.095   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      12.129  -3.507   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       4.160  -1.380   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       7.365  -1.108   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.016  -5.061   0.000  0.00  0.00           O+0
CONECT    1   11                                                            
CONECT    2   11                                                            
CONECT    3    4   11                                                       
CONECT    4    3   12                                                       
CONECT    5    6   13                                                       
CONECT    6    5   15                                                       
CONECT    7   12   14                                                       
CONECT    8   13   18                                                       
CONECT    9   16   17                                                       
CONECT   10   20   24                                                       
CONECT   11    1    2    3                                                  
CONECT   12    4    7   16                                                  
CONECT   13    5    8   21                                                  
CONECT   14    7   17   19                                                  
CONECT   15    6   18   20                                                  
CONECT   16    9   12   22                                                  
CONECT   17    9   14   24                                                  
CONECT   18    8   15   25                                                  
CONECT   19   14   20   25                                                  
CONECT   20   10   15   19   23                                             
CONECT   21   13                                                            
CONECT   22   16                                                            
CONECT   23   20                                                            
CONECT   24   10   17                                                       
CONECT   25   18   19                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

Download
3D PDB for NP0048937 (Glyceollidin II)
Download
SMILES for NP0048937 (Glyceollidin II)
CC(C)=CCC1=CC2=C(OCC3(O)C2OC2=C3C=CC(O)=C2)C=C1O
Download
INCHI for NP0048937 (Glyceollidin II)
InChI=1S/C20H20O5/c1-11(2)3-4-12-7-14-17(9-16(12)22)24-10-20(23)15-6-5-13(21)8-18(15)25-19(14)20/h3,5-9,19,21-23H,4,10H2,1-2H3
Download
View in JSmol
Synonyms
ValueSource
2-(3-Methyl-2-butenyl)-6H-benzofuro[3,2-c][1]benzopyran-3,6a,9(11ah)-triol, 9ciHMDB
GlyceocarpinHMDB
Chemical FormulaC20H20O5
Average Mass340.3698 Da
Monoisotopic Mass340.13107 Da
IUPAC Name4-(3-methylbut-2-en-1-yl)-8,17-dioxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-2(7),3,5,11(16),12,14-hexaene-5,10,14-triol
Traditional Name4-(3-methylbut-2-en-1-yl)-8,17-dioxatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-2(7),3,5,11(16),12,14-hexaene-5,10,14-triol
CAS Registry Number77979-22-7
SMILES
CC(C)=CCC1=CC2=C(OCC3(O)C2OC2=C3C=CC(O)=C2)C=C1O
InChI Identifier
InChI=1S/C20H20O5/c1-11(2)3-4-12-7-14-17(9-16(12)22)24-10-20(23)15-6-5-13(21)8-18(15)25-19(14)20/h3,5-9,19,21-23H,4,10H2,1-2H3
InChI KeyTUXXPRXOVFCNPC-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Glycine maxFooDB
Taxus fuanaPlant
Taxus wallichiana var. yunnanensisPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pterocarpans. These are benzo-pyrano-furano-benzene compounds, containing the  6H-[1]benzofuro[3,2-c]chromene skeleton. They are derivatives of isoflavonoids.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassIsoflavonoids  
Sub ClassFuranoisoflavonoids  
Direct ParentPterocarpans  
Alternative Parents
Substituents
  • Pterocarpan
    • 

  • Isoflavanol
    • 

  • Isoflavan
    • 

  • Chromane
    • 

  • Benzopyran
    • 

  • 1-benzopyran
    • 

  • Coumaran
    • 

  • Benzofuran
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Alkyl aryl ether
    • 

  • Benzenoid
    • 

  • Tertiary alcohol
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Ether
    • 

  • Polyol
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic 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
logP2.83ALOGPS
logP3.44ChemAxon
logS-3.9ALOGPS
pKa (Strongest Acidic)8.99ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area79.15 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity93.91 m³·mol⁻¹ChemAxon
Polarizability36.6 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0037916  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB017073  
KNApSAcK IDC00009688  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound85206973  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available