NP-MRD: Showing NP-Card for Rhamnellaflavoside C (NP0026989)

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Record Information

Version

2.0

Created at

2021-06-19 18:44:22 UTC

Updated at

2021-06-29 23:52:51 UTC

NP-MRD ID

NP0026989

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rhamnellaflavoside C

Provided By

JEOL Database JEOL Logo

Description

Rhamnellaflavoside C is found in Rhamnella inaequilatera. Rhamnellaflavoside C was first documented in 2004 (Takeda, Y., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192120443D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306192120443D          

 70 74  0  0  0  0            999 V2000
   -3.7681    8.9961   -1.2581 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0026989

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C(C(O[H])=C2C(=O)C([H])=C(OC2=C1[H])C1=C([H])C([H])=C(O[C@]2([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])C([H])=C1[H])[C@]1([H])O[C@]([H])(C([H])([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])C1([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C27H30O13/c1-10-22(32)15(31)8-17(37-10)20-14(30)7-18-21(24(20)34)13(29)6-16(39-18)11-2-4-12(5-3-11)38-27-26(36)25(35)23(33)19(9-28)40-27/h2-7,10,15,17,19,22-23,25-28,30-36H,8-9H2,1H3/t10-,15-,17-,19-,22-,23-,25+,26-,27-/m1/s1

> <INCHI_KEY>
SJJKJSJCDCJFNW-HLDRAWRKSA-N

> <FORMULA>
C27H30O13

> <MOLECULAR_WEIGHT>
562.524

> <EXACT_MASS>
562.168641026

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
57.57106839587736

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[(2R,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]-5,7-dihydroxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-4H-chromen-4-one

> <ALOGPS_LOGP>
0.08

> <JCHEM_LOGP>
-0.5814952170000001

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.778021153644921

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.162386962515959

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092343686506

> <JCHEM_POLAR_SURFACE_AREA>
215.82999999999998

> <JCHEM_REFRACTIVITY>
135.53580000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.75e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-[(2R,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]-5,7-dihydroxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 70 74  0  0  0  0  0  0  0  0999 V2000
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   -6.4271    4.3804   -1.2120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8400    5.3109    0.1510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9447    6.4442   -2.4690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4407    5.6791   -0.9170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9657    7.9657   -0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6564    8.7752   -1.3204 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  4  1  0
 39 40  1  0
 37 38  1  0
 24 25  1  0
  6  5  2  0
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  9  8  2  0
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 35 64  1  0
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      -3.768   8.996  -1.258  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.576   7.767  -1.660  0.00  0.00           C+0
HETATM    3  O   UNK     0      -3.875   6.612  -1.171  0.00  0.00           O+0
HETATM    4  C   UNK     0      -4.509   5.379  -1.567  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.662   4.193  -1.137  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.712   4.257  -0.104  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.439   5.415   0.570  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.981   3.137   0.297  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.180   1.918  -0.341  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.428   0.855   0.092  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.607  -0.376  -0.519  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.741  -1.446   0.015  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.226  -2.742   0.242  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.389  -3.735   0.759  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.939  -3.449   1.076  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.670  -4.508   1.541  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.793  -4.194   2.380  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.973  -3.993   1.594  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.506  -5.149   0.926  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.232  -5.074  -0.584  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.917  -5.502  -0.916  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.086  -6.493   1.544  0.00  0.00           C+0
HETATM   23  O   UNK     0       5.018  -7.533   1.222  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.050  -6.312   3.055  0.00  0.00           C+0
HETATM   25  O   UNK     0       3.801  -7.565   3.709  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.954  -5.317   3.438  0.00  0.00           C+0
HETATM   27  O   UNK     0       3.285  -4.774   4.730  0.00  0.00           O+0
HETATM   28  C   UNK     0       1.437  -2.168   0.845  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.599  -1.173   0.328  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.464  -0.599  -1.526  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.288   0.514  -2.016  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.096   0.364  -2.927  0.00  0.00           O+0
HETATM   33  C   UNK     0      -3.109   1.821  -1.371  0.00  0.00           C+0
HETATM   34  C   UNK     0      -3.849   2.947  -1.765  0.00  0.00           C+0
HETATM   35  O   UNK     0      -4.784   2.875  -2.770  0.00  0.00           O+0
HETATM   36  C   UNK     0      -5.907   5.308  -0.946  0.00  0.00           C+0
HETATM   37  C   UNK     0      -6.732   6.506  -1.395  0.00  0.00           C+0
HETATM   38  O   UNK     0      -7.998   6.526  -0.727  0.00  0.00           O+0
HETATM   39  C   UNK     0      -5.999   7.817  -1.087  0.00  0.00           C+0
HETATM   40  O   UNK     0      -6.742   8.906  -1.641  0.00  0.00           O+0
HETATM   41  H   UNK     0      -2.749   8.927  -1.655  0.00  0.00           H+0
HETATM   42  H   UNK     0      -3.675   9.064  -0.169  0.00  0.00           H+0
HETATM   43  H   UNK     0      -4.223   9.918  -1.630  0.00  0.00           H+0
HETATM   44  H   UNK     0      -4.606   7.732  -2.757  0.00  0.00           H+0
HETATM   45  H   UNK     0      -4.566   5.385  -2.664  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.859   6.146   0.067  0.00  0.00           H+0
HETATM   47  H   UNK     0      -1.257   3.226   1.102  0.00  0.00           H+0
HETATM   48  H   UNK     0      -2.263  -2.995   0.033  0.00  0.00           H+0
HETATM   49  H   UNK     0      -0.782  -4.736   0.923  0.00  0.00           H+0
HETATM   50  H   UNK     0       2.605  -3.262   2.929  0.00  0.00           H+0
HETATM   51  H   UNK     0       5.594  -5.045   1.031  0.00  0.00           H+0
HETATM   52  H   UNK     0       4.925  -5.727  -1.123  0.00  0.00           H+0
HETATM   53  H   UNK     0       4.360  -4.052  -0.956  0.00  0.00           H+0
HETATM   54  H   UNK     0       2.299  -4.884  -0.480  0.00  0.00           H+0
HETATM   55  H   UNK     0       3.101  -6.831   1.202  0.00  0.00           H+0
HETATM   56  H   UNK     0       4.851  -7.782   0.293  0.00  0.00           H+0
HETATM   57  H   UNK     0       5.029  -5.980   3.424  0.00  0.00           H+0
HETATM   58  H   UNK     0       4.389  -8.204   3.257  0.00  0.00           H+0
HETATM   59  H   UNK     0       1.995  -5.831   3.574  0.00  0.00           H+0
HETATM   60  H   UNK     0       3.407  -5.547   5.315  0.00  0.00           H+0
HETATM   61  H   UNK     0       2.475  -1.915   1.040  0.00  0.00           H+0
HETATM   62  H   UNK     0       1.010  -0.179   0.160  0.00  0.00           H+0
HETATM   63  H   UNK     0      -2.587  -1.554  -2.020  0.00  0.00           H+0
HETATM   64  H   UNK     0      -4.790   1.955  -3.124  0.00  0.00           H+0
HETATM   65  H   UNK     0      -6.427   4.380  -1.212  0.00  0.00           H+0
HETATM   66  H   UNK     0      -5.840   5.311   0.151  0.00  0.00           H+0
HETATM   67  H   UNK     0      -6.945   6.444  -2.469  0.00  0.00           H+0
HETATM   68  H   UNK     0      -8.441   5.679  -0.917  0.00  0.00           H+0
HETATM   69  H   UNK     0      -5.966   7.966  -0.000  0.00  0.00           H+0
HETATM   70  H   UNK     0      -7.656   8.775  -1.320  0.00  0.00           H+0
CONECT    1    2   41   42   43                                             
CONECT    2   39    3    1   44                                             
CONECT    3    4    2                                                       
CONECT    4    3   36    5   45                                             
CONECT    5    6   34    4                                                  
CONECT    6    5    8    7                                                  
CONECT    7    6   46                                                       
CONECT    8    9    6   47                                                  
CONECT    9    8   33   10                                                  
CONECT   10   11    9                                                       
CONECT   11   30   10   12                                                  
CONECT   12   13   29   11                                                  
CONECT   13   12   14   48                                                  
CONECT   14   13   15   49                                                  
CONECT   15   14   28   16                                                  
CONECT   16   17   15                                                       
CONECT   17   26   18   16   50                                             
CONECT   18   17   19                                                       
CONECT   19   18   22   20   51                                             
CONECT   20   21   19   52   53                                             
CONECT   21   20   54                                                       
CONECT   22   24   19   23   55                                             
CONECT   23   22   56                                                       
CONECT   24   25   22   26   57                                             
CONECT   25   24   58                                                       
CONECT   26   24   17   27   59                                             
CONECT   27   26   60                                                       
CONECT   28   15   29   61                                                  
CONECT   29   28   12   62                                                  
CONECT   30   31   11   63                                                  
CONECT   31   33   30   32                                                  
CONECT   32   31                                                            
CONECT   33   34    9   31                                                  
CONECT   34    5   33   35                                                  
CONECT   35   34   64                                                       
CONECT   36    4   37   65   66                                             
CONECT   37   38   36   39   67                                             
CONECT   38   37   68                                                       
CONECT   39   40   37    2   69                                             
CONECT   40   39   70                                                       
CONECT   41    1                                                            
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    2                                                            
CONECT   45    4                                                            
CONECT   46    7                                                            
CONECT   47    8                                                            
CONECT   48   13                                                            
CONECT   49   14                                                            
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   25                                                            
CONECT   59   26                                                            
CONECT   60   27                                                            
CONECT   61   28                                                            
CONECT   62   29                                                            
CONECT   63   30                                                            
CONECT   64   35                                                            
CONECT   65   36                                                            
CONECT   66   36                                                            
CONECT   67   37                                                            
CONECT   68   38                                                            
CONECT   69   39                                                            
CONECT   70   40                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  148    0
END

RDKit          3D

70 74  0  0  0  0  0  0  0  0999 V2000
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 36 37  1  0
 28 29  2  0
 29 12  1  0
 11 12  1  0
 37 39  1  0
  6  7  1  0
 15 16  1  0
 39  2  1  0
 31 32  2  0
  2  3  1  0
 34 35  1  0
 22 23  1  0
 19 20  1  0
  2  1  1  0
  4  5  1  0
 23 56  1  0
 22 55  1  6
 17 50  1  1
 20 52  1  0
 20 53  1  0
 19 51  1  6
 26 59  1  1
 27 60  1  0
 24 57  1  1
 25 58  1  0
 21 54  1  0
 40 70  1  0
  4 45  1  6
 39 69  1  1
 37 67  1  6
 38 68  1  0
 36 65  1  0
 36 66  1  0
  1 41  1  0
  1 42  1  0
  1 43  1  0
  2 44  1  6
  8 47  1  0
 30 63  1  0
 13 48  1  0
 14 49  1  0
 28 61  1  0
 29 62  1  0
  7 46  1  0
 35 64  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₀O₁₃

Average Mass

562.5240 Da

Monoisotopic Mass

562.16864 Da

IUPAC Name

6-[(2R,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]-5,7-dihydroxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-4H-chromen-4-one

Traditional Name

6-[(2R,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]-5,7-dihydroxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one

CAS Registry Number

Not Available

SMILES

[H]OC1=C(C(O[H])=C2C(=O)C([H])=C(OC2=C1[H])C1=C([H])C([H])=C(O[C@]2([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])C([H])=C1[H])[C@]1([H])O[C@]([H])(C([H])([H])[H])[C@@]([H])(O[H])[C@]([H])(O[H])C1([H])[H]

InChI Identifier

InChI=1S/C27H30O13/c1-10-22(32)15(31)8-17(37-10)20-14(30)7-18-21(24(20)34)13(29)6-16(39-18)11-2-4-12(5-3-11)38-27-26(36)25(35)23(33)19(9-28)40-27/h2-7,10,15,17,19,22-23,25-28,30-36H,8-9H2,1H3/t10-,15-,17-,19-,22-,23-,25+,26-,27-/m1/s1

InChI Key

SJJKJSJCDCJFNW-HLDRAWRKSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, C₅D₅N (H) / CD₃OD (C), simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, C₅D₅N (H) / CD₃OD (C), 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
Rhamnella inaequilatera	JEOL database	Takeda, Y., et al, Phytochemistry 65, 463 (2004)

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	0.08	ALOGPS
logP	-0.58	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	6.16	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	215.83 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	135.54 m³·mol⁻¹	ChemAxon
Polarizability	57.57 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	No	ChemAxon

External Links

Not Available

References

General References

Takeda, Y., et al. (2004). Takeda, Y., et al, Phytochemistry 65, 463 (2004). Phytochem..

Showing NP-Card for Rhamnellaflavoside C (NP0026989)

MOL for NP0026989 (Rhamnellaflavoside C)

3D MOL for NP0026989 (Rhamnellaflavoside C)

3D SDF for NP0026989 (Rhamnellaflavoside C)

3D-SDF for NP0026989 (Rhamnellaflavoside C)

PDB for NP0026989 (Rhamnellaflavoside C)

3D PDB for NP0026989 (Rhamnellaflavoside C)

SMILES for NP0026989 (Rhamnellaflavoside C)

INCHI for NP0026989 (Rhamnellaflavoside C)

Structure for NP0026989 (Rhamnellaflavoside C)

3D Structure for NP0026989 (Rhamnellaflavoside C)