NP-MRD: Showing NP-Card for Wubangziside A (NP0077361)

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Record Information

Version

2.0

Created at

2022-04-28 22:31:12 UTC

Updated at

2022-04-28 22:31:12 UTC

NP-MRD ID

NP0077361

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Wubangziside A

Description

7-{[(2S,3R,4R,5R,6R)-6-({[(2R,3R,4S)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-1-hydroxy-9H-xanthen-9-one 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. Wubangziside A is found in Polygala caudata. Based on a literature review very few articles have been published on 7-{[(2S,3R,4R,5R,6R)-6-({[(2R,3R,4S)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-1-hydroxy-9H-xanthen-9-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292200312D          

 37 41  0  0  1  0            999 V2000
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 36 37  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292200312D          

 37 41  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0077361

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@]1(O)CO[C@@H](OC[C@H]2O[C@@H](OC3=CC=C4OC5=CC=CC(O)=C5C(=O)C4=C3)[C@H](O)[C@H](O)[C@H]2O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H26O13/c25-8-24(32)9-34-23(21(24)31)33-7-15-18(28)19(29)20(30)22(37-15)35-10-4-5-13-11(6-10)17(27)16-12(26)2-1-3-14(16)36-13/h1-6,15,18-23,25-26,28-32H,7-9H2/t15-,18+,19-,20-,21+,22-,23-,24+/m1/s1

> <INCHI_KEY>
XXNLZBROTQYGNV-IWACPHONSA-N

> <FORMULA>
C24H26O13

> <MOLECULAR_WEIGHT>
522.459

> <EXACT_MASS>
522.137340897

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
49.861006577224465

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.38

> <JCHEM_LOGP>
-0.5420575763333331

> <ALOGPS_LOGS>
-2.34

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.701909537713409

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.41385907938566

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423790163389214

> <JCHEM_POLAR_SURFACE_AREA>
204.82999999999998

> <JCHEM_REFRACTIVITY>
119.59270000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.36e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-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  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -6.581   7.065   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -6.105   8.530   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.565   8.530   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -4.089   7.065   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -7.505   9.171   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -6.282  10.060   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -7.695  10.671   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -8.045   6.589   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -6.668   2.310   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2    6   36                                                  
CONECT    2    1    3   33                                                  
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                                                       
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10    4                                                       
CONECT   12    9   13                                                       
CONECT   13   12   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   29                                                  
CONECT   23   22   24   26   27                                             
CONECT   24   23   25                                                       
CONECT   25   24   21                                                       
CONECT   26   23                                                            
CONECT   27   23   28                                                       
CONECT   28   27                                                            
CONECT   29   22                                                            
CONECT   30   16                                                            
CONECT   31   15                                                            
CONECT   32   14                                                            
CONECT   33    2   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35    1   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₆O₁₃

Average Mass

522.4590 Da

Monoisotopic Mass

522.13734 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC[C@]1(O)CO[C@@H](OC[C@H]2O[C@@H](OC3=CC=C4OC5=CC=CC(O)=C5C(=O)C4=C3)[C@H](O)[C@H](O)[C@H]2O)[C@@H]1O

InChI Identifier

InChI=1S/C24H26O13/c25-8-24(32)9-34-23(21(24)31)33-7-15-18(28)19(29)20(30)22(37-15)35-10-4-5-13-11(6-10)17(27)16-12(26)2-1-3-14(16)36-13/h1-6,15,18-23,25-26,28-32H,7-9H2/t15-,18+,19-,20-,21+,22-,23-,24+/m1/s1

InChI Key

XXNLZBROTQYGNV-IWACPHONSA-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 caudata	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
Chromone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Benzenoid
Pyran
Oxane
Heteroaromatic compound
Vinylogous acid
Tetrahydrofuran
Tertiary alcohol
Secondary alcohol
Oxacycle
Polyol
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
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	-0.38	ALOGPS
logP	-0.54	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	8.41	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	204.83 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	119.59 m³·mol⁻¹	ChemAxon
Polarizability	49.86 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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162950783

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Wubangziside A (NP0077361)

MOL for NP0077361 (Wubangziside A)

3D MOL for NP0077361 (Wubangziside A)

3D SDF for NP0077361 (Wubangziside A)

3D-SDF for NP0077361 (Wubangziside A)

PDB for NP0077361 (Wubangziside A)

3D PDB for NP0077361 (Wubangziside A)

SMILES for NP0077361 (Wubangziside A)

INCHI for NP0077361 (Wubangziside A)

Structure for NP0077361 (Wubangziside A)

3D Structure for NP0077361 (Wubangziside A)