NP-MRD: Showing NP-Card for Polygalaxanthone III (NP0075685)

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Record Information

Version

2.0

Created at

2022-04-28 20:56:18 UTC

Updated at

2022-04-28 20:56:18 UTC

NP-MRD ID

NP0075685

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Polygalaxanthone III

Description

Polygalaxanthone III 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. Polygalaxanthone III is found in Polygala sibirica and Polygala tenuifolia Willd. . Polygalaxanthone III was first documented in 2018 (PMID: 29577615). Based on a literature review a small amount of articles have been published on Polygalaxanthone III (PMID: 31354847) (PMID: 34384566) (PMID: 33603068) (PMID: 31685751).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282222562D          

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M  END

     RDKit          3D

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 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 13 18  1  0  0  0  0
 17 19  1  1  0  0  0
 19 20  1  0  0  0  0
 21 20  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 21 25  1  0  0  0  0
 25 26  1  1  0  0  0
 24 27  1  1  0  0  0
 24 28  1  6  0  0  0
 28 29  1  0  0  0  0
 16 30  1  6  0  0  0
 15 31  1  1  0  0  0
 14 32  1  6  0  0  0
  8 33  1  0  0  0  0
  2 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
  1 37  2  0  0  0  0
 36 38  1  0  0  0  0
 38 39  1  0  0  0  0
 35 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0075685

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=C2OC3=CC(O)=C([C@@H]4O[C@H](CO[C@@H]5OC[C@](O)(CO)[C@H]5O)[C@@H](O)[C@H](O)[C@H]4O)C(O)=C3C(=O)C2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O15/c1-36-12-2-8-11(3-9(12)27)39-13-4-10(28)15(19(31)16(13)17(8)29)22-21(33)20(32)18(30)14(40-22)5-37-24-23(34)25(35,6-26)7-38-24/h2-4,14,18,20-24,26-28,30-35H,5-7H2,1H3/t14-,18-,20+,21-,22+,23+,24-,25-/m1/s1

> <INCHI_KEY>
LLJUCXMVRPAONX-AYATVRNWSA-N

> <FORMULA>
C25H28O15

> <MOLECULAR_WEIGHT>
568.484

> <EXACT_MASS>
568.142820202

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
54.682041479102125

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2S,3R,4R,5S,6R)-6-({[(2R,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]-1,3,6-trihydroxy-7-methoxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
-0.46

> <JCHEM_LOGP>
-1.492546975333334

> <ALOGPS_LOGS>
-2.08

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.912029608243668

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.047315373927697

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6450214781817962

> <JCHEM_POLAR_SURFACE_AREA>
245.28999999999996

> <JCHEM_REFRACTIVITY>
129.0107

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.77e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2S,3R,4R,5S,6R)-6-({[(2R,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]-1,3,6-trihydroxy-7-methoxyxanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   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  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667  -3.080   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      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -8.002   0.000   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -9.409  -0.626   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0     -10.439   0.518   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -9.669   1.852   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.163   1.532   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -7.019   2.562   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0     -10.906   2.770   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -9.524   3.385   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -8.124   4.026   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
CONECT    1    2    6   37                                                  
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9   33                                                  
CONECT    9    8   10   13                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10    4                                                       
CONECT   12   10                                                            
CONECT   13    9   14   18                                                  
CONECT   14   13   15   32                                                  
CONECT   15   14   16   31                                                  
CONECT   16   15   17   30                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17   13                                                       
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   25                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   27   28                                             
CONECT   25   24   21   26                                                  
CONECT   26   25                                                            
CONECT   27   24                                                            
CONECT   28   24   29                                                       
CONECT   29   28                                                            
CONECT   30   16                                                            
CONECT   31   15                                                            
CONECT   32   14                                                            
CONECT   33    8                                                            
CONECT   34    2   35                                                       
CONECT   35   34   36   40                                                  
CONECT   36   35   37   38                                                  
CONECT   37   36    1                                                       
CONECT   38   36   39                                                       
CONECT   39   38                                                            
CONECT   40   35                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Value	Source
Polygala-xanthone III	MeSH

Chemical Formula

C₂₅H₂₈O₁₅

Average Mass

568.4840 Da

Monoisotopic Mass

568.14282 Da

IUPAC Name

2-[(2S,3R,4R,5S,6R)-6-({[(2R,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]-1,3,6-trihydroxy-7-methoxy-9H-xanthen-9-one

Traditional Name

2-[(2S,3R,4R,5S,6R)-6-({[(2R,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]-1,3,6-trihydroxy-7-methoxyxanthen-9-one

CAS Registry Number

Not Available

SMILES

COC1=C(O)C=C2OC3=CC(O)=C([C@@H]4O[C@H](CO[C@@H]5OC[C@](O)(CO)[C@H]5O)[C@@H](O)[C@H](O)[C@H]4O)C(O)=C3C(=O)C2=C1

InChI Identifier

InChI=1S/C25H28O15/c1-36-12-2-8-11(3-9(12)27)39-13-4-10(28)15(19(31)16(13)17(8)29)22-21(33)20(32)18(30)14(40-22)5-37-24-23(34)25(35,6-26)7-38-24/h2-4,14,18,20-24,26-28,30-35H,5-7H2,1H3/t14-,18-,20+,21-,22+,23+,24-,25-/m1/s1

InChI Key

LLJUCXMVRPAONX-AYATVRNWSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Polygala sibirica	Plant	KNApSAcK
Polygala tenuifolia	Plant	KNApSAcK

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

Phenolic glycoside
Xanthone
O-glycosyl compound
Glycosyl compound
Disaccharide
C-glycosyl compound
Chromone
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Pyran
Oxane
Benzenoid
Oxolane
Tertiary alcohol
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Acetal
Oxacycle
Dialkyl ether
Ether
Polyol
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Primary alcohol
Organic oxide
Organooxygen 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	-0.46	ALOGPS
logP	-1.5	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	7.05	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	245.29 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	129.01 m³·mol⁻¹	ChemAxon
Polarizability	54.68 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	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

C00037665

Chemspider ID

9344158

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11169063

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ba Y, Wang M, Zhang K, Chen Q, Wang J, Lv H, Jiang Y, Shi R: Intestinal Absorption Profile of Three Polygala Oligosaccharide Esters in Polygalae Radix and the Effects of Other Components in Polygalae Radix on Their Absorption. Evid Based Complement Alternat Med. 2019 Jul 2;2019:1379531. doi: 10.1155/2019/1379531. eCollection 2019. [PubMed:31354847 ]
Wu Y, Fu H, Yang X, Leng F, Huang Y, Deng H, Xiang Q, Zhang S: Polygalaxanthone III downregulates inflammation in the lipopolysaccharide-stimulated RAW264.7 macrophages: A quantibody array analysis. J Pharmacol Sci. 2021 Oct;147(2):184-191. doi: 10.1016/j.jphs.2021.06.010. Epub 2021 Jul 3. [PubMed:34384566 ]
Opo FADM, Rahman MM, Ahammad F, Ahmed I, Bhuiyan MA, Asiri AM: Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein. Sci Rep. 2021 Feb 18;11(1):4049. doi: 10.1038/s41598-021-83626-x. [PubMed:33603068 ]
Tsujimoto T, Nishihara M, Osumi Y, Hakamatsuka T, Goda Y, Uchiyama N, Ozeki Y: Structural Analysis of Polygalaxanthones, C-Glucosyl Xanthones of Polygala tenuifolia Roots. Chem Pharm Bull (Tokyo). 2019;67(11):1242-1247. doi: 10.1248/cpb.c19-00608. [PubMed:31685751 ]
Shi Y, Cao C, Zhu Y, Gao T, Yang W, Liu Mingzhu Qi M, Huang R, Qian D, Duan JA: Comparative pharmacokinetic study of the components of Jia-Wei-Kai-Xin-San in normal and vascular dementia rats by ultra-fast liquid chromatography coupled with tandem mass spectrometry. J Sep Sci. 2018 Jun;41(12):2504-2516. doi: 10.1002/jssc.201701144. Epub 2018 Apr 23. [PubMed:29577615 ]

Showing NP-Card for Polygalaxanthone III (NP0075685)

MOL for NP0075685 (Polygalaxanthone III)

3D MOL for NP0075685 (Polygalaxanthone III)

3D SDF for NP0075685 (Polygalaxanthone III)

3D-SDF for NP0075685 (Polygalaxanthone III)

PDB for NP0075685 (Polygalaxanthone III)

3D PDB for NP0075685 (Polygalaxanthone III)

SMILES for NP0075685 (Polygalaxanthone III)

INCHI for NP0075685 (Polygalaxanthone III)

Structure for NP0075685 (Polygalaxanthone III)

3D Structure for NP0075685 (Polygalaxanthone III)