NP-MRD: Showing NP-Card for glucofrangulin B (NP0030516)

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Record Information

Version

2.0

Created at

2021-06-19 21:51:19 UTC

Updated at

2021-06-29 23:58:31 UTC

NP-MRD ID

NP0030516

Secondary Accession Numbers

None

Natural Product Identification

Common Name

glucofrangulin B

Provided By

JEOL Database JEOL Logo

Description

glucofrangulin B is found in Frangula alnus, frangula Rhamnus and Rumex crispus. glucofrangulin B was first documented in 1998 (Francis, G. W., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192123513D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306192123513D          

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M  END
> <DATABASE_ID>
NP0030516

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C(=C([H])C2=C1C(=O)C1=C(O[C@@]3([H])O[C@@]([H])(C([H])([H])O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]3([H])O[H])C([H])=C(O[C@]3([H])OC([H])([H])[C@](O[H])(C([H])([H])O[H])[C@@]3([H])O[H])C([H])=C1C2=O)C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O14/c1-9-2-11-16(13(29)3-9)20(32)17-12(18(11)30)4-10(38-25-23(35)26(36,7-28)8-37-25)5-14(17)39-24-22(34)21(33)19(31)15(6-27)40-24/h2-5,15,19,21-25,27-29,31,33-36H,6-8H2,1H3/t15-,19-,21+,22-,23-,24-,25-,26+/m0/s1

> <INCHI_KEY>
RFPVGIKRAIIMPG-VLOIXPIOSA-N

> <FORMULA>
C26H28O14

> <MOLECULAR_WEIGHT>
564.496

> <EXACT_MASS>
564.147905582

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
56.28035068829327

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-8-hydroxy-6-methyl-1-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9,10-dihydroanthracene-9,10-dione

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
-0.8703681020000003

> <ALOGPS_LOGS>
-2.29

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.6957303584224

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.295990295759223

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923462808114

> <JCHEM_POLAR_SURFACE_AREA>
232.89999999999998

> <JCHEM_REFRACTIVITY>
130.68060000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.92e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-8-hydroxy-6-methyl-1-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}anthracene-9,10-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 68 72  0  0  0  0  0  0  0  0999 V2000
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M  END

HEADER    PROTEIN                                 19-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-21         0                                  
HETATM    1  C   UNK     0       0.050   5.375  -6.816  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.148   4.955  -5.389  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.033   5.888  -4.353  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.189   5.489  -3.026  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.069   6.477  -2.086  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.447   4.149  -2.705  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.547   3.216  -3.733  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.394   3.615  -5.071  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.813   1.798  -3.431  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.929   0.986  -4.341  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.918   1.361  -2.024  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.130  -0.003  -1.757  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.192  -0.459  -0.443  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.378  -1.751  -0.041  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.564  -2.748  -1.048  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.797  -2.600  -1.769  0.00  0.00           O+0
HETATM   17  C   UNK     0      -3.386  -3.910  -1.928  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.385  -4.927  -1.388  0.00  0.00           C+0
HETATM   19  O   UNK     0      -1.466  -5.313  -2.433  0.00  0.00           O+0
HETATM   20  C   UNK     0      -3.030  -6.200  -0.850  0.00  0.00           C+0
HETATM   21  O   UNK     0      -3.719  -6.877  -1.901  0.00  0.00           O+0
HETATM   22  C   UNK     0      -1.651  -4.109  -0.346  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.376  -4.680  -0.044  0.00  0.00           O+0
HETATM   24  C   UNK     0      -1.044   0.456   0.600  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.865   1.820   0.340  0.00  0.00           C+0
HETATM   26  O   UNK     0      -0.656   2.684   1.381  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.765   2.764   2.295  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.564   1.855   3.383  0.00  0.00           O+0
HETATM   29  C   UNK     0      -2.619   1.915   4.350  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.389   0.832   5.412  0.00  0.00           C+0
HETATM   31  O   UNK     0      -3.506   0.693   6.283  0.00  0.00           O+0
HETATM   32  C   UNK     0      -2.671   3.312   4.988  0.00  0.00           C+0
HETATM   33  O   UNK     0      -3.729   3.408   5.947  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.875   4.357   3.892  0.00  0.00           C+0
HETATM   35  O   UNK     0      -2.824   5.666   4.482  0.00  0.00           O+0
HETATM   36  C   UNK     0      -1.811   4.220   2.804  0.00  0.00           C+0
HETATM   37  O   UNK     0      -2.133   5.151   1.759  0.00  0.00           O+0
HETATM   38  C   UNK     0      -0.793   2.282  -0.983  0.00  0.00           C+0
HETATM   39  C   UNK     0      -0.619   3.722  -1.301  0.00  0.00           C+0
HETATM   40  O   UNK     0      -0.639   4.585  -0.425  0.00  0.00           O+0
HETATM   41  H   UNK     0      -0.266   6.413  -6.966  0.00  0.00           H+0
HETATM   42  H   UNK     0       1.106   5.284  -7.090  0.00  0.00           H+0
HETATM   43  H   UNK     0      -0.547   4.754  -7.492  0.00  0.00           H+0
HETATM   44  H   UNK     0       0.175   6.933  -4.572  0.00  0.00           H+0
HETATM   45  H   UNK     0      -0.236   6.082  -1.202  0.00  0.00           H+0
HETATM   46  H   UNK     0      -0.469   2.874  -5.867  0.00  0.00           H+0
HETATM   47  H   UNK     0      -1.243  -0.686  -2.597  0.00  0.00           H+0
HETATM   48  H   UNK     0      -0.717  -2.740  -1.747  0.00  0.00           H+0
HETATM   49  H   UNK     0      -3.612  -4.055  -2.989  0.00  0.00           H+0
HETATM   50  H   UNK     0      -4.321  -3.906  -1.358  0.00  0.00           H+0
HETATM   51  H   UNK     0      -0.643  -5.577  -1.970  0.00  0.00           H+0
HETATM   52  H   UNK     0      -2.273  -6.890  -0.461  0.00  0.00           H+0
HETATM   53  H   UNK     0      -3.748  -5.987  -0.052  0.00  0.00           H+0
HETATM   54  H   UNK     0      -3.095  -6.904  -2.654  0.00  0.00           H+0
HETATM   55  H   UNK     0      -2.227  -4.032   0.585  0.00  0.00           H+0
HETATM   56  H   UNK     0       0.070  -4.056   0.561  0.00  0.00           H+0
HETATM   57  H   UNK     0      -1.052   0.093   1.625  0.00  0.00           H+0
HETATM   58  H   UNK     0      -2.705   2.528   1.773  0.00  0.00           H+0
HETATM   59  H   UNK     0      -3.578   1.699   3.859  0.00  0.00           H+0
HETATM   60  H   UNK     0      -2.212  -0.136   4.931  0.00  0.00           H+0
HETATM   61  H   UNK     0      -1.498   1.052   6.012  0.00  0.00           H+0
HETATM   62  H   UNK     0      -3.790   1.600   6.530  0.00  0.00           H+0
HETATM   63  H   UNK     0      -1.734   3.524   5.520  0.00  0.00           H+0
HETATM   64  H   UNK     0      -3.814   4.368   6.133  0.00  0.00           H+0
HETATM   65  H   UNK     0      -3.880   4.267   3.463  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.783   6.285   3.723  0.00  0.00           H+0
HETATM   67  H   UNK     0      -0.832   4.520   3.199  0.00  0.00           H+0
HETATM   68  H   UNK     0      -1.484   4.989   1.034  0.00  0.00           H+0
CONECT    1    2   41   42   43                                             
CONECT    2    8    3    1                                                  
CONECT    3    2    4   44                                                  
CONECT    4    6    3    5                                                  
CONECT    5    4   45                                                       
CONECT    6   39    7    4                                                  
CONECT    7    9    6    8                                                  
CONECT    8    7    2   46                                                  
CONECT    9   11    7   10                                                  
CONECT   10    9                                                            
CONECT   11   12   38    9                                                  
CONECT   12   13   11   47                                                  
CONECT   13   24   12   14                                                  
CONECT   14   15   13                                                       
CONECT   15   22   14   16   48                                             
CONECT   16   17   15                                                       
CONECT   17   16   18   49   50                                             
CONECT   18   22   17   19   20                                             
CONECT   19   18   51                                                       
CONECT   20   21   18   52   53                                             
CONECT   21   20   54                                                       
CONECT   22   18   15   23   55                                             
CONECT   23   22   56                                                       
CONECT   24   13   25   57                                                  
CONECT   25   24   38   26                                                  
CONECT   26   25   27                                                       
CONECT   27   36   28   26   58                                             
CONECT   28   27   29                                                       
CONECT   29   28   32   30   59                                             
CONECT   30   31   29   60   61                                             
CONECT   31   30   62                                                       
CONECT   32   34   29   33   63                                             
CONECT   33   32   64                                                       
CONECT   34   35   32   36   65                                             
CONECT   35   34   66                                                       
CONECT   36   34   27   37   67                                             
CONECT   37   36   68                                                       
CONECT   38   25   11   39                                                  
CONECT   39   38    6   40                                                  
CONECT   40   39                                                            
CONECT   41    1                                                            
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    3                                                            
CONECT   45    5                                                            
CONECT   46    8                                                            
CONECT   47   12                                                            
CONECT   48   15                                                            
CONECT   49   17                                                            
CONECT   50   17                                                            
CONECT   51   19                                                            
CONECT   52   20                                                            
CONECT   53   20                                                            
CONECT   54   21                                                            
CONECT   55   22                                                            
CONECT   56   23                                                            
CONECT   57   24                                                            
CONECT   58   27                                                            
CONECT   59   29                                                            
CONECT   60   30                                                            
CONECT   61   30                                                            
CONECT   62   31                                                            
CONECT   63   32                                                            
CONECT   64   33                                                            
CONECT   65   34                                                            
CONECT   66   35                                                            
CONECT   67   36                                                            
CONECT   68   37                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  144    0
END

RDKit          3D

68 72  0  0  0  0  0  0  0  0999 V2000
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M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₁₄

Average Mass

564.4960 Da

Monoisotopic Mass

564.14791 Da

IUPAC Name

3-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-8-hydroxy-6-methyl-1-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9,10-dihydroanthracene-9,10-dione

Traditional Name

3-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-8-hydroxy-6-methyl-1-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}anthracene-9,10-dione

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C(=C([H])C2=C1C(=O)C1=C(O[C@@]3([H])O[C@@]([H])(C([H])([H])O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]3([H])O[H])C([H])=C(O[C@]3([H])OC([H])([H])[C@](O[H])(C([H])([H])O[H])[C@@]3([H])O[H])C([H])=C1C2=O)C([H])([H])[H]

InChI Identifier

InChI=1S/C26H28O14/c1-9-2-11-16(13(29)3-9)20(32)17-12(18(11)30)4-10(38-25-23(35)26(36,7-28)8-37-25)5-14(17)39-24-22(34)21(33)19(31)15(6-27)40-24/h2-5,15,19,21-25,27-29,31,33-36H,6-8H2,1H3/t15-,19-,21+,22-,23-,24-,25-,26+/m0/s1

InChI Key

RFPVGIKRAIIMPG-VLOIXPIOSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, DMSO-d6 , simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Frangula alnus	LOTUS Database	35616633
frangula Rhamnus	JEOL database	Francis, G. W., et al, Magn. Reson. Chem. 36, 769 (1998)
Rumex crispus	LOTUS Database	35616633

Chemical Taxonomy

Classification

Not classified

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	-0.47	ALOGPS
logP	-0.87	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	8.3	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	232.9 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	130.68 m³·mol⁻¹	ChemAxon
Polarizability	56.28 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

Not Available

References

General References

Francis, G. W., et al. (1998). Francis, G. W., et al, Magn. Reson. Chem. 36, 769 (1998). Mag. Reson. Chem..

Showing NP-Card for glucofrangulin B (NP0030516)

MOL for NP0030516 (glucofrangulin B)

3D MOL for NP0030516 (glucofrangulin B)

3D SDF for NP0030516 (glucofrangulin B)

3D-SDF for NP0030516 (glucofrangulin B)

PDB for NP0030516 (glucofrangulin B)

3D PDB for NP0030516 (glucofrangulin B)

SMILES for NP0030516 (glucofrangulin B)

INCHI for NP0030516 (glucofrangulin B)

Structure for NP0030516 (glucofrangulin B)

3D Structure for NP0030516 (glucofrangulin B)