NP-MRD: Showing NP-Card for 1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one (NP0295637)

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Record Information

Version

2.0

Created at

2022-09-10 04:43:50 UTC

Updated at

2022-09-10 04:43:50 UTC

NP-MRD ID

NP0295637

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one

Description

Wubangziside A 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-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one was first documented in 1984 (PMID: 6549569). Based on a literature review very few articles have been published on Wubangziside A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102206432D          

 37 41  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309102206432D          

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 14 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 12 36  1  0  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0295637

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1CC(O)(CO)OC1OCC1OC(OC2=CC=C3OC4=CC=CC(O)=C4C(=O)C3=C2)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O12/c1-11-8-25(32,10-26)37-23(11)33-9-17-20(29)21(30)22(31)24(36-17)34-12-5-6-15-13(7-12)19(28)18-14(27)3-2-4-16(18)35-15/h2-7,11,17,20-24,26-27,29-32H,8-10H2,1H3

> <INCHI_KEY>
XTCXFMKCQXHXFT-UHFFFAOYSA-N

> <FORMULA>
C25H28O12

> <MOLECULAR_WEIGHT>
520.487

> <EXACT_MASS>
520.158076342

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
50.781614362277345

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}-9H-xanthen-9-one

> <JCHEM_LOGP>
1.2641696596666683

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.192270067065326

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.413358699262742

> <JCHEM_PKA_STRONGEST_BASIC>
-3.413843008458196

> <JCHEM_POLAR_SURFACE_AREA>
184.6

> <JCHEM_REFRACTIVITY>
123.0628

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.684 -14.882   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.828 -13.852   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.335 -14.172   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.105 -12.838   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -6.351 -13.743   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -6.135 -11.694   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.659 -10.229   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -4.074 -11.694   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6    8                                             
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6                                                            
CONECT    8    4    9                                                       
CONECT    9    8    2   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   36                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   32                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   31                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   30                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   21   28                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   19   31                                                  
CONECT   31   30   16                                                       
CONECT   32   14   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   12   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Value	Source
Euxanthone-7-O-apiofuranosyl(1-6)glucopyranoside	MeSH

Chemical Formula

C₂₅H₂₈O₁₂

Average Mass

520.4870 Da

Monoisotopic Mass

520.15808 Da

IUPAC Name

1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}-9H-xanthen-9-one

Traditional Name

1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one

CAS Registry Number

Not Available

SMILES

CC1CC(O)(CO)OC1OCC1OC(OC2=CC=C3OC4=CC=CC(O)=C4C(=O)C3=C2)C(O)C(O)C1O

InChI Identifier

InChI=1S/C25H28O12/c1-11-8-25(32,10-26)37-23(11)33-9-17-20(29)21(30)22(31)24(36-17)34-12-5-6-15-13(7-12)19(28)18-14(27)3-2-4-16(18)35-15/h2-7,11,17,20-24,26-27,29-32H,8-10H2,1H3

InChI Key

XTCXFMKCQXHXFT-UHFFFAOYSA-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

Not Available

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
Chromone
Glycosyl compound
O-glycosyl compound
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Monosaccharide
Oxane
Pyran
Benzenoid
Heteroaromatic compound
Oxolane
Vinylogous acid
Hemiacetal
Secondary alcohol
Polyol
Acetal
Oxacycle
Primary alcohol
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
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	1.26	ChemAxon
pKa (Strongest Acidic)	8.41	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	184.6 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	123.06 m³·mol⁻¹	ChemAxon
Polarizability	50.78 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

C00040666

Chemspider ID

4589165

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5486994

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Pan MD, Mao Q: [Isolation and identification of wubangziside A and B from Polygala caudata Rehd et Wils]. Yao Xue Xue Bao. 1984 Dec;19(12):899-903. [PubMed:6549569 ]
LOTUS database [Link]

Showing NP-Card for 1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one (NP0295637)

MOL for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

3D MOL for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

3D SDF for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

3D-SDF for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

PDB for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

3D PDB for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

SMILES for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

INCHI for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

Structure for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)

3D Structure for NP0295637 (1-hydroxy-7-{[3,4,5-trihydroxy-6-({[5-hydroxy-5-(hydroxymethyl)-3-methyloxolan-2-yl]oxy}methyl)oxan-2-yl]oxy}xanthen-9-one)