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Showing NP-Card for Garcinone E (NP0047607)

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Record Information
Version2.0
Created at2022-03-17 20:42:57 UTC
Updated at2022-03-17 20:42:57 UTC
NP-MRD IDNP0047607
Secondary Accession NumbersNone
Natural Product Identification
Common NameGarcinone E
DescriptionGarcinone E belongs to the class of organic compounds known as 8-prenylated xanthones. These are organic compounds containing a C5-isoprenoid group linked to a xanthone moiety at the 8-position. Xanthone is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring that carries a ketone group. Garcinone E is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Garcinone E has been detected, but not quantified in, fruits and purple mangosteens. Garcinone E is found in Garcina xipshuanbannaensis, Garcinia costata, Garcinia xipshuanbannaensis and Pentadesma butyracea. This could make garcinone e a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0047607 (Garcinone E)


  Mrv0541 05061307032D          

 34 36  0  0  0  0            999 V2000
    7.1447    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    4.9500    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
    2.8579   -1.6500    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
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    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
    5.7158    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    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
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    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
    5.0013    2.0625    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
    1.4289    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
    3.5724    1.2375    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
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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    2.4750    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
    5.7158    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 10  7  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 14  1  1  0  0  0  0
 14  2  1  0  0  0  0
 14  7  2  0  0  0  0
 15  3  1  0  0  0  0
 15  4  1  0  0  0  0
 15  8  2  0  0  0  0
 16  5  1  0  0  0  0
 16  6  1  0  0  0  0
 16  9  2  0  0  0  0
 17 10  1  0  0  0  0
 18 11  1  0  0  0  0
 19 12  1  0  0  0  0
 20 13  2  0  0  0  0
 20 17  1  0  0  0  0
 21 13  1  0  0  0  0
 22 18  1  0  0  0  0
 23 21  2  0  0  0  0
 24 17  2  0  0  0  0
 24 23  1  0  0  0  0
 25 18  2  0  0  0  0
 26 19  2  0  0  0  0
 26 25  1  0  0  0  0
 27 22  1  0  0  0  0
 27 23  1  0  0  0  0
 28 19  1  0  0  0  0
 28 22  2  0  0  0  0
 29 20  1  0  0  0  0
 30 24  1  0  0  0  0
 31 25  1  0  0  0  0
 32 26  1  0  0  0  0
 33 27  2  0  0  0  0
 34 21  1  0  0  0  0
 34 28  1  0  0  0  0
M  END
Download

3D MOL for NP0047607 (Garcinone E)

Download
3D SDF for NP0047607 (Garcinone E)

  Mrv0541 05061307032D          

 34 36  0  0  0  0            999 V2000
    7.1447    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    4.9500    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
    2.8579   -1.6500    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
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    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
    5.7158    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    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
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    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
    5.0013    2.0625    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
    1.4289    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
    3.5724    1.2375    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
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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    2.4750    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
    5.7158    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 10  7  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 14  1  1  0  0  0  0
 14  2  1  0  0  0  0
 14  7  2  0  0  0  0
 15  3  1  0  0  0  0
 15  4  1  0  0  0  0
 15  8  2  0  0  0  0
 16  5  1  0  0  0  0
 16  6  1  0  0  0  0
 16  9  2  0  0  0  0
 17 10  1  0  0  0  0
 18 11  1  0  0  0  0
 19 12  1  0  0  0  0
 20 13  2  0  0  0  0
 20 17  1  0  0  0  0
 21 13  1  0  0  0  0
 22 18  1  0  0  0  0
 23 21  2  0  0  0  0
 24 17  2  0  0  0  0
 24 23  1  0  0  0  0
 25 18  2  0  0  0  0
 26 19  2  0  0  0  0
 26 25  1  0  0  0  0
 27 22  1  0  0  0  0
 27 23  1  0  0  0  0
 28 19  1  0  0  0  0
 28 22  2  0  0  0  0
 29 20  1  0  0  0  0
 30 24  1  0  0  0  0
 31 25  1  0  0  0  0
 32 26  1  0  0  0  0
 33 27  2  0  0  0  0
 34 21  1  0  0  0  0
 34 28  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047607

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC1=C(O)C2=C(OC3=C(C2=O)C(CC=C(C)C)=C(O)C(O)=C3CC=C(C)C)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O6/c1-14(2)7-10-17-20(29)13-21-23(24(17)30)27(33)22-18(11-8-15(3)4)25(31)26(32)19(28(22)34-21)12-9-16(5)6/h7-9,13,29-32H,10-12H2,1-6H3

> <INCHI_KEY>
WVJYEKGQSBGNRP-UHFFFAOYSA-N

> <FORMULA>
C28H32O6

> <MOLECULAR_WEIGHT>
464.5501

> <EXACT_MASS>
464.219888756

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
52.89416526208363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,6,8-tetrahydroxy-1,4,7-tris(3-methylbut-2-en-1-yl)-9H-xanthen-9-one

> <ALOGPS_LOGP>
5.15

> <JCHEM_LOGP>
7.581079931666667

> <ALOGPS_LOGS>
-5.01

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.677910129674154

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.0618452210078475

> <JCHEM_PKA_STRONGEST_BASIC>
-4.232218157753214

> <JCHEM_POLAR_SURFACE_AREA>
107.22000000000001

> <JCHEM_REFRACTIVITY>
137.46829999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.51e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
garcinone E

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0047607 (Garcinone E)
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PDB for NP0047607 (Garcinone E)
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      13.337   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.671   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   9.240   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
CONECT    1   14                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4   15                                                            
CONECT    5   16                                                            
CONECT    6   16                                                            
CONECT    7   10   14                                                       
CONECT    8   11   15                                                       
CONECT    9   12   16                                                       
CONECT   10    7   17                                                       
CONECT   11    8   18                                                       
CONECT   12    9   19                                                       
CONECT   13   20   21                                                       
CONECT   14    1    2    7                                                  
CONECT   15    3    4    8                                                  
CONECT   16    5    6    9                                                  
CONECT   17   10   20   24                                                  
CONECT   18   11   22   25                                                  
CONECT   19   12   26   28                                                  
CONECT   20   13   17   29                                                  
CONECT   21   13   23   34                                                  
CONECT   22   18   27   28                                                  
CONECT   23   21   24   27                                                  
CONECT   24   17   23   30                                                  
CONECT   25   18   26   31                                                  
CONECT   26   19   25   32                                                  
CONECT   27   22   23   33                                                  
CONECT   28   19   22   34                                                  
CONECT   29   20                                                            
CONECT   30   24                                                            
CONECT   31   25                                                            
CONECT   32   26                                                            
CONECT   33   27                                                            
CONECT   34   21   28                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

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3D PDB for NP0047607 (Garcinone E)
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SMILES for NP0047607 (Garcinone E)
CC(C)=CCC1=C(O)C2=C(OC3=C(C2=O)C(CC=C(C)C)=C(O)C(O)=C3CC=C(C)C)C=C1O
Download
INCHI for NP0047607 (Garcinone E)
InChI=1S/C28H32O6/c1-14(2)7-10-17-20(29)13-21-23(24(17)30)27(33)22-18(11-8-15(3)4)25(31)26(32)19(28(22)34-21)12-9-16(5)6/h7-9,13,29-32H,10-12H2,1-6H3
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View in JSmol
Synonyms
ValueSource
Garcinone eMeSH
Chemical FormulaC28H32O6
Average Mass464.5501 Da
Monoisotopic Mass464.21989 Da
IUPAC Name2,3,6,8-tetrahydroxy-1,4,7-tris(3-methylbut-2-en-1-yl)-9H-xanthen-9-one
Traditional Namegarcinone E
CAS Registry Number112649-21-5
SMILES
CC(C)=CCC1=C(O)C2=C(OC3=C(C2=O)C(CC=C(C)C)=C(O)C(O)=C3CC=C(C)C)C=C1O
InChI Identifier
InChI=1S/C28H32O6/c1-14(2)7-10-17-20(29)13-21-23(24(17)30)27(33)22-18(11-8-15(3)4)25(31)26(32)19(28(22)34-21)12-9-16(5)6/h7-9,13,29-32H,10-12H2,1-6H3
InChI KeyWVJYEKGQSBGNRP-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Garcina xipshuanbannaensis-
Garcinia costataLOTUS Database
Garcinia mangostanaFooDB
Garcinia xipshuanbannaensisPlant
Pentadesma butyraceaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 8-prenylated xanthones. These are organic compounds containing a C5-isoprenoid group linked to a xanthone moiety at the 8-position. Xanthone is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring that carries a ketone group.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassBenzopyrans  
Sub Class1-benzopyrans  
Direct Parent8-prenylated xanthones  
Alternative Parents
Substituents
  • 2-prenylated xanthone
    • 

  • 4-prenylated xanthone
    • 

  • 8-prenylated xanthone
    • 

  • Chromone
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Pyranone
    • 

  • Pyran
    • 

  • Benzenoid
    • 

  • Heteroaromatic compound
    • 

  • Vinylogous acid
    • 

  • Oxacycle
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
logP5.15ALOGPS
logP7.58ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)7.06ChemAxon
pKa (Strongest Basic)-4.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area107.22 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity137.47 m³·mol⁻¹ChemAxon
Polarizability52.89 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDHMDB0033316  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB011340  
KNApSAcK IDC00030359  
Chemspider ID8473979  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10298511  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available