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Showing NP-Card for Isoginkgetin (NP0047792)

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Record Information
Version2.0
Created at2022-03-17 20:46:03 UTC
Updated at2022-03-17 20:46:03 UTC
NP-MRD IDNP0047792
Secondary Accession NumbersNone
Natural Product Identification
Common NameIsoginkgetin
DescriptionIsoginkgetin, also known as sciadopitysin, belongs to the class of organic compounds known as biflavonoids and polyflavonoids. These are organic compounds containing at least two flavan/flavone units. These units are usually linked through CC or C-O-C bonds. Some examples include C2-O-C3, C2-O-C4, C3'-C3''', and C6-C8''. Isoginkgetin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Isoginkgetin has been detected, but not quantified in, fats and oils and ginkgo nuts. Isoginkgetin is found in Podocarpus gracilior, Bowenia spp., Callitropsis nootkatensis, Cycas circinalis, Dacrydium spp., Decussocarpus spp., Encephalartos spp., Epimedium koreanum , Halocarpus spp., Lepidozamia spp., Podocarpus nagi , Podocarpus elongatus and Podocarpus macrophyllus. Isoginkgetin was first documented in 2006 (PMID: 17121913). This could make isoginkgetin a potential biomarker for the consumption of these foods (PMID: 17761896) (PMID: 18826947) (PMID: 23624148).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0047792 (Isoginkgetin)


  Mrv0541 05061307272D          

 42 47  0  0  0  0            999 V2000
    7.8592   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    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
    5.7158    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    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
    0.0000   -2.4750    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
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    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
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 42 32  1  0  0  0  0
M  END
Download

3D MOL for NP0047792 (Isoginkgetin)

Download
3D SDF for NP0047792 (Isoginkgetin)

  Mrv0541 05061307272D          

 42 47  0  0  0  0            999 V2000
    7.8592   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    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
    5.7158    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    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
    0.0000   -2.4750    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
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    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
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    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
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    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
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  5  2  0  0  0  0
 15  3  2  0  0  0  0
 15  4  1  0  0  0  0
 16  5  1  0  0  0  0
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 17 10  2  0  0  0  0
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 18  7  1  0  0  0  0
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 20 10  1  0  0  0  0
 21 12  2  0  0  0  0
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 23 13  1  0  0  0  0
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 29 19  1  0  0  0  0
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 33 17  1  0  0  0  0
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 35 21  1  0  0  0  0
 36 22  1  0  0  0  0
 37 23  2  0  0  0  0
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 39  1  1  0  0  0  0
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 42 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047792

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C=C1)C1=CC(=O)C2=C(O)C=C(O)C(=C2O1)C1=C(OC)C=CC(=C1)C1=CC(=O)C2=C(O)C=C(O)C=C2O1

> <INCHI_IDENTIFIER>
InChI=1S/C32H22O10/c1-39-18-6-3-15(4-7-18)26-14-24(38)31-22(36)12-21(35)29(32(31)42-26)19-9-16(5-8-25(19)40-2)27-13-23(37)30-20(34)10-17(33)11-28(30)41-27/h3-14,33-36H,1-2H3

> <INCHI_KEY>
HUOOMAOYXQFIDQ-UHFFFAOYSA-N

> <FORMULA>
C32H22O10

> <MOLECULAR_WEIGHT>
566.5111

> <EXACT_MASS>
566.121296924

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
57.73076614032937

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8-[5-(5,7-dihydroxy-4-oxo-4H-chromen-2-yl)-2-methoxyphenyl]-5,7-dihydroxy-2-(4-methoxyphenyl)-4H-chromen-4-one

> <ALOGPS_LOGP>
4.97

> <JCHEM_LOGP>
5.379145925333332

> <ALOGPS_LOGS>
-5.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.795930016269367

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.125371094953871

> <JCHEM_PKA_STRONGEST_BASIC>
-4.54468047524327

> <JCHEM_POLAR_SURFACE_AREA>
151.98

> <JCHEM_REFRACTIVITY>
153.8706

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.97e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-[5-(5,7-dihydroxy-4-oxochromen-2-yl)-2-methoxyphenyl]-5,7-dihydroxy-2-(4-methoxyphenyl)chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0047792 (Isoginkgetin)
Download
PDB for NP0047792 (Isoginkgetin)
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      14.671  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.003  -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  -7.700   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      13.337  -3.080   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
CONECT    1   39                                                            
CONECT    2   40                                                            
CONECT    3    6   15                                                       
CONECT    4    7   15                                                       
CONECT    5    8   16                                                       
CONECT    6    3   18                                                       
CONECT    7    4   18                                                       
CONECT    8    5   25                                                       
CONECT    9   16   19                                                       
CONECT   10   17   20                                                       
CONECT   11   17   28                                                       
CONECT   12   21   22                                                       
CONECT   13   23   27                                                       
CONECT   14   24   26                                                       
CONECT   15    3    4   26                                                  
CONECT   16    5    9   27                                                  
CONECT   17   10   11   33                                                  
CONECT   18    6    7   39                                                  
CONECT   19    9   25   29                                                  
CONECT   20   10   30   34                                                  
CONECT   21   12   29   35                                                  
CONECT   22   12   31   36                                                  
CONECT   23   13   30   37                                                  
CONECT   24   14   31   38                                                  
CONECT   25    8   19   40                                                  
CONECT   26   14   15   42                                                  
CONECT   27   13   16   41                                                  
CONECT   28   11   30   41                                                  
CONECT   29   19   21   32                                                  
CONECT   30   20   23   28                                                  
CONECT   31   22   24   32                                                  
CONECT   32   29   31   42                                                  
CONECT   33   17                                                            
CONECT   34   20                                                            
CONECT   35   21                                                            
CONECT   36   22                                                            
CONECT   37   23                                                            
CONECT   38   24                                                            
CONECT   39    1   18                                                       
CONECT   40    2   25                                                       
CONECT   41   27   28                                                       
CONECT   42   26   32                                                       
MASTER        0    0    0    0    0    0    0    0   42    0   94    0
END

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3D PDB for NP0047792 (Isoginkgetin)
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SMILES for NP0047792 (Isoginkgetin)
COC1=CC=C(C=C1)C1=CC(=O)C2=C(O)C=C(O)C(=C2O1)C1=C(OC)C=CC(=C1)C1=CC(=O)C2=C(O)C=C(O)C=C2O1
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INCHI for NP0047792 (Isoginkgetin)
InChI=1S/C32H22O10/c1-39-18-6-3-15(4-7-18)26-14-24(38)31-22(36)12-21(35)29(32(31)42-26)19-9-16(5-8-25(19)40-2)27-13-23(37)30-20(34)10-17(33)11-28(30)41-27/h3-14,33-36H,1-2H3
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View in JSmol
Synonyms
ValueSource
4',4'''-dimethylamentoflavoneChEBI
Iso-ginkgetinChEBI
SciadopitysinHMDB
Chemical FormulaC32H22O10
Average Mass566.5111 Da
Monoisotopic Mass566.12130 Da
IUPAC Name8-[5-(5,7-dihydroxy-4-oxo-4H-chromen-2-yl)-2-methoxyphenyl]-5,7-dihydroxy-2-(4-methoxyphenyl)-4H-chromen-4-one
Traditional Name8-[5-(5,7-dihydroxy-4-oxochromen-2-yl)-2-methoxyphenyl]-5,7-dihydroxy-2-(4-methoxyphenyl)chromen-4-one
CAS Registry Number548-19-6
SMILES
COC1=CC=C(C=C1)C1=CC(=O)C2=C(O)C=C(O)C(=C2O1)C1=C(OC)C=CC(=C1)C1=CC(=O)C2=C(O)C=C(O)C=C2O1
InChI Identifier
InChI=1S/C32H22O10/c1-39-18-6-3-15(4-7-18)26-14-24(38)31-22(36)12-21(35)29(32(31)42-26)19-9-16(5-8-25(19)40-2)27-13-23(37)30-20(34)10-17(33)11-28(30)41-27/h3-14,33-36H,1-2H3
InChI KeyHUOOMAOYXQFIDQ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Afrocarpus graciliorPlant
Bowenia spp.Plant
Callitropsis nootkatensisLOTUS Database
Cycas circinalisLOTUS Database
Dacrydium spp.Plant
Decussocarpus spp.Plant
Encephalartos spp.Plant
Epimedium koreanumPlant
Ginkgo bilobaFooDB
Halocarpus spp.Plant
Lepidozamia spp.Plant
Nageia nagiPlant
Podocarpus elongatusPlant
Podocarpus macrophyllusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as biflavonoids and polyflavonoids. These are organic compounds containing at least two flavan/flavone units. These units are usually linked through CC or C-O-C bonds. Some examples include C2-O-C3, C2-O-C4, C3'-C3''', and C6-C8''.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassFlavonoids  
Sub ClassBiflavonoids and polyflavonoids  
Direct ParentBiflavonoids and polyflavonoids  
Alternative Parents
Substituents
  • Bi- and polyflavonoid skeleton
    • 

  • 4p-methoxyflavonoid-skeleton
    • 

  • 5-hydroxyflavonoid
    • 

  • 7-hydroxyflavonoid
    • 

  • Flavone
    • 

  • Hydroxyflavonoid
    • 

  • Chromone
    • 

  • Benzopyran
    • 

  • 1-benzopyran
    • 

  • Phenoxy compound
    • 

  • Anisole
    • 

  • Methoxybenzene
    • 

  • Phenol ether
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Alkyl aryl ether
    • 

  • Pyranone
    • 

  • Monocyclic benzene moiety
    • 

  • Benzenoid
    • 

  • Pyran
    • 

  • Vinylogous acid
    • 

  • Heteroaromatic compound
    • 

  • Organoheterocyclic compound
    • 

  • Ether
    • 

  • Oxacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organic oxygen 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
logP4.97ALOGPS
logP5.38ChemAxon
logS-5.3ALOGPS
pKa (Strongest Acidic)6.13ChemAxon
pKa (Strongest Basic)-4.5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area151.98 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity153.87 m³·mol⁻¹ChemAxon
Polarizability57.73 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0033937  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012143  
KNApSAcK IDC00006494  
Chemspider ID4477111  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5318569  
PDB IDNot Available
ChEBI ID79087  
Good Scents IDNot Available
References
General References
  1. Yoon SO, Shin S, Lee HJ, Chun HK, Chung AS: Isoginkgetin inhibits tumor cell invasion by regulating phosphatidylinositol 3-kinase/Akt-dependent matrix metalloproteinase-9 expression. Mol Cancer Ther. 2006 Nov;5(11):2666-75. doi: 10.1158/1535-7163.MCT-06-0321. [PubMed:17121913  ] 
  2. Liu G, Grifman M, Macdonald J, Moller P, Wong-Staal F, Li QX: Isoginkgetin enhances adiponectin secretion from differentiated adiposarcoma cells via a novel pathway involving AMP-activated protein kinase. J Endocrinol. 2007 Sep;194(3):569-78. doi: 10.1677/JOE-07-0200. [PubMed:17761896  ] 
  3. O'Brien K, Matlin AJ, Lowell AM, Moore MJ: The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing. J Biol Chem. 2008 Nov 28;283(48):33147-54. doi: 10.1074/jbc.M805556200. Epub 2008 Sep 30. [PubMed:18826947  ] 
  4. Suh KS, Lee YS, Kim YS, Choi EM: Sciadopitysin protects osteoblast function via its antioxidant activity in MC3T3-E1 cells. Food Chem Toxicol. 2013 Aug;58:220-7. doi: 10.1016/j.fct.2013.04.028. Epub 2013 Apr 23. [PubMed:23624148  ]