NP-MRD: Showing NP-Card for 1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione (NP0287802)

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Record Information

Version

2.0

Created at

2022-09-09 17:12:38 UTC

Updated at

2022-09-09 17:12:38 UTC

NP-MRD ID

NP0287802

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione

Description

Garcinianone B belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. 1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione is found in Garcinia multiflora. Based on a literature review very few articles have been published on garcinianone B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092219122D          

 34 36  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309092219122D          

 34 36  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0287802

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC\C(C)=C/CC1(CC=C(C)C)C(=O)C(O)=CC2=C1C(=O)C1=C(O)C=C(O)C=C1O2

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O6/c1-16(2)7-6-8-18(5)10-12-28(11-9-17(3)4)25-23(15-21(31)27(28)33)34-22-14-19(29)13-20(30)24(22)26(25)32/h7,9-10,13-15,29-31H,6,8,11-12H2,1-5H3/b18-10-

> <INCHI_KEY>
FZFFGBOPCQADGY-ZDLGFXPLSA-N

> <FORMULA>
C28H32O6

> <MOLECULAR_WEIGHT>
464.558

> <EXACT_MASS>
464.21988875

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
51.046330860349265

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)-2,9-dihydro-1H-xanthene-2,9-dione

> <JCHEM_LOGP>
6.458199891

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.783152156077453

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.516449662842538

> <JCHEM_PKA_STRONGEST_BASIC>
-4.3287833985739335

> <JCHEM_POLAR_SURFACE_AREA>
104.06

> <JCHEM_REFRACTIVITY>
137.57829999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.518  -8.127   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.002  -8.394   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.012  -7.215   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.475  -9.841   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.041 -10.109   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.031  -8.929   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.548  -9.197   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.075 -10.644   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.538  -8.017   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.011  -6.570   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.991  -6.570   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.464  -8.017   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.454  -9.197   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.927 -10.644   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.971  -8.929   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   17   34                                             
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   11   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23   34                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   31                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   24   32                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   22   11                                                  
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₂O₆

Average Mass

464.5580 Da

Monoisotopic Mass

464.21989 Da

IUPAC Name

1-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)-2,9-dihydro-1H-xanthene-2,9-dione

Traditional Name

1-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C/CC1(CC=C(C)C)C(=O)C(O)=CC2=C1C(=O)C1=C(O)C=C(O)C=C1O2

InChI Identifier

InChI=1S/C28H32O6/c1-16(2)7-6-8-18(5)10-12-28(11-9-17(3)4)25-23(15-21(31)27(28)33)34-22-14-19(29)13-20(30)24(22)26(25)32/h7,9-10,13-15,29-31H,6,8,11-12H2,1-5H3/b18-10-

InChI Key

FZFFGBOPCQADGY-ZDLGFXPLSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Garcinia multiflora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Xanthone
Chromone
Aromatic monoterpenoid
Monoterpenoid
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Ketone
Cyclic ketone
Oxacycle
Enol
Polyol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	6.46	ChemAxon
pKa (Strongest Acidic)	6.52	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.06 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	137.58 m³·mol⁻¹	ChemAxon
Polarizability	51.05 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00044779

Chemspider ID

10195645

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

135442127

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione (NP0287802)

MOL for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

3D MOL for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

3D SDF for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

3D-SDF for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

PDB for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

3D PDB for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

SMILES for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

INCHI for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

Structure for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)

3D Structure for NP0287802 (1-[(2z)-3,7-dimethylocta-2,6-dien-1-yl]-3,6,8-trihydroxy-1-(3-methylbut-2-en-1-yl)xanthene-2,9-dione)