NP-MRD: Showing NP-Card for Gymnasterone C (NP0007406)

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Record Information

Version

2.0

Created at

2020-12-09 04:14:28 UTC

Updated at

2021-07-15 16:57:30 UTC

NP-MRD ID

NP0007406

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gymnasterone C

Provided By

NPAtlas

Description

Gymnasterone C is found in Gymnascella and Gymnascella dankaliensis. Based on a literature review very few articles have been published on gymnasterone C.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242121123D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306242121123D          

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  2 34  1  6  0  0  0
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 30 70  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0007406

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@]1([H])C([H])=C2C([H])=C([H])C3=C4C(=O)C([H])([H])[C@]([H])([C@@]([H])(C(\[H])=C(/[H])[C@]([H])(C([H])([H])[H])C([H])(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])[C@@]4(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3([H])[C@@]2(C([H])([H])[H])C([H])([H])C1([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O2/c1-17(2)18(3)7-8-19(4)24-16-25(30)26-22-10-9-20-15-21(29)11-13-27(20,5)23(22)12-14-28(24,26)6/h7-10,15,17-19,21,23-24,29H,11-14,16H2,1-6H3/b8-7+/t18-,19+,21-,23-,24+,27-,28+/m0/s1

> <INCHI_KEY>
XRXZKBAAJAKIMB-AXOAYYPZSA-N

> <FORMULA>
C28H40O2

> <MOLECULAR_WEIGHT>
408.626

> <EXACT_MASS>
408.302830528

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
49.88274256501562

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,5S,14R,15R)-14-[(2R,3E,5R)-5,6-dimethylhept-3-en-2-yl]-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-6,8,10-trien-12-one

> <ALOGPS_LOGP>
5.72

> <JCHEM_LOGP>
5.715451606333335

> <ALOGPS_LOGS>
-5.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.72031295069909

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.593314696769905

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6643430971568547

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
128.52089999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.53e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5S,14R,15R)-14-[(2R,3E,5R)-5,6-dimethylhept-3-en-2-yl]-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-6,8,10-trien-12-one

> <JCHEM_VEBER_RULE>
1

$$$$

     RDKit          3D

 70 73  0  0  0  0  0  0  0  0999 V2000
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   -1.4432   -1.7500   -1.3405 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0604   -0.3307   -2.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0151    1.0897   -2.1924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7422   -0.4884   -2.5569 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  6
 24 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  6
 29 10  1  0
 29 14  1  0
 26 15  1  0
 24 18  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
  2 34  1  6
  3 35  1  0
  3 36  1  0
  3 37  1  0
  4 38  1  1
  5 39  1  0
  5 40  1  0
  5 41  1  0
  6 42  1  0
  7 43  1  0
  8 44  1  6
  9 45  1  0
  9 46  1  0
  9 47  1  0
 10 48  1  1
 11 49  1  0
 11 50  1  0
 16 51  1  0
 17 52  1  0
 19 53  1  0
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 22 56  1  0
 22 57  1  0
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 27 64  1  0
 27 65  1  0
 28 66  1  0
 28 67  1  0
 30 68  1  0
 30 69  1  0
 30 70  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       8.068   0.641   0.843  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.783  -0.046   0.374  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.640  -1.341   1.151  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.593   0.848   0.677  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.779   2.154  -0.056  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.377   0.187   0.131  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.337  -0.108   0.866  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.141  -0.784   0.213  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.932  -2.111   0.963  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.933   0.071   0.369  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.248   1.477  -0.280  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.115   2.067  -0.413  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.465   3.233  -0.740  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.087   0.984  -0.071  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.281   0.947   0.370  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.983   2.231   0.639  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.307   2.166   0.718  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.062   0.923   0.558  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.327   0.896   0.917  0.00  0.00           C+0
HETATM   20  C   UNK     0      -7.216  -0.278   0.819  0.00  0.00           C+0
HETATM   21  O   UNK     0      -8.463   0.134   0.336  0.00  0.00           O+0
HETATM   22  C   UNK     0      -6.608  -1.353   0.004  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.148  -1.521   0.397  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.357  -0.308  -0.009  0.00  0.00           C+0
HETATM   25  C   UNK     0      -4.273  -0.233  -1.508  0.00  0.00           C+0
HETATM   26  C   UNK     0      -3.034  -0.319   0.682  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.197  -1.506   0.624  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.024  -1.468  -0.292  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.268  -0.240  -0.445  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.056   0.020  -1.951  0.00  0.00           C+0
HETATM   31  H   UNK     0       8.905  -0.075   0.769  0.00  0.00           H+0
HETATM   32  H   UNK     0       8.206   1.526   0.168  0.00  0.00           H+0
HETATM   33  H   UNK     0       7.891   1.003   1.865  0.00  0.00           H+0
HETATM   34  H   UNK     0       6.836  -0.248  -0.710  0.00  0.00           H+0
HETATM   35  H   UNK     0       6.043  -1.137   2.077  0.00  0.00           H+0
HETATM   36  H   UNK     0       7.617  -1.784   1.417  0.00  0.00           H+0
HETATM   37  H   UNK     0       6.050  -2.095   0.577  0.00  0.00           H+0
HETATM   38  H   UNK     0       5.555   0.994   1.763  0.00  0.00           H+0
HETATM   39  H   UNK     0       4.793   2.644  -0.191  0.00  0.00           H+0
HETATM   40  H   UNK     0       6.248   2.015  -1.053  0.00  0.00           H+0
HETATM   41  H   UNK     0       6.456   2.784   0.565  0.00  0.00           H+0
HETATM   42  H   UNK     0       4.388  -0.047  -0.931  0.00  0.00           H+0
HETATM   43  H   UNK     0       3.304   0.111   1.905  0.00  0.00           H+0
HETATM   44  H   UNK     0       2.314  -1.021  -0.833  0.00  0.00           H+0
HETATM   45  H   UNK     0       1.096  -2.059   1.675  0.00  0.00           H+0
HETATM   46  H   UNK     0       2.839  -2.311   1.607  0.00  0.00           H+0
HETATM   47  H   UNK     0       1.790  -2.963   0.281  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.638   0.261   1.411  0.00  0.00           H+0
HETATM   49  H   UNK     0       1.832   2.072   0.432  0.00  0.00           H+0
HETATM   50  H   UNK     0       1.754   1.315  -1.228  0.00  0.00           H+0
HETATM   51  H   UNK     0      -2.423   3.155   0.758  0.00  0.00           H+0
HETATM   52  H   UNK     0      -4.833   3.115   0.916  0.00  0.00           H+0
HETATM   53  H   UNK     0      -6.738   1.853   1.325  0.00  0.00           H+0
HETATM   54  H   UNK     0      -7.326  -0.672   1.876  0.00  0.00           H+0
HETATM   55  H   UNK     0      -8.900   0.607   1.096  0.00  0.00           H+0
HETATM   56  H   UNK     0      -7.103  -2.316   0.262  0.00  0.00           H+0
HETATM   57  H   UNK     0      -6.695  -1.112  -1.076  0.00  0.00           H+0
HETATM   58  H   UNK     0      -4.787  -2.411  -0.160  0.00  0.00           H+0
HETATM   59  H   UNK     0      -5.104  -1.752   1.469  0.00  0.00           H+0
HETATM   60  H   UNK     0      -4.238  -1.238  -1.943  0.00  0.00           H+0
HETATM   61  H   UNK     0      -5.217   0.268  -1.856  0.00  0.00           H+0
HETATM   62  H   UNK     0      -3.410   0.370  -1.841  0.00  0.00           H+0
HETATM   63  H   UNK     0      -3.297  -0.164   1.791  0.00  0.00           H+0
HETATM   64  H   UNK     0      -2.819  -2.397   0.310  0.00  0.00           H+0
HETATM   65  H   UNK     0      -1.798  -1.834   1.629  0.00  0.00           H+0
HETATM   66  H   UNK     0      -0.397  -2.342  -0.056  0.00  0.00           H+0
HETATM   67  H   UNK     0      -1.443  -1.750  -1.341  0.00  0.00           H+0
HETATM   68  H   UNK     0       1.060  -0.331  -2.211  0.00  0.00           H+0
HETATM   69  H   UNK     0      -0.015   1.090  -2.192  0.00  0.00           H+0
HETATM   70  H   UNK     0      -0.742  -0.488  -2.557  0.00  0.00           H+0
CONECT    1    2   31   32   33                                             
CONECT    2    1    3    4   34                                             
CONECT    3    2   35   36   37                                             
CONECT    4    2    5    6   38                                             
CONECT    5    4   39   40   41                                             
CONECT    6    4    7   42                                                  
CONECT    7    6    8   43                                                  
CONECT    8    7    9   10   44                                             
CONECT    9    8   45   46   47                                             
CONECT   10    8   11   29   48                                             
CONECT   11   10   12   49   50                                             
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   29                                                  
CONECT   15   14   16   26                                                  
CONECT   16   15   17   51                                                  
CONECT   17   16   18   52                                                  
CONECT   18   17   19   24                                                  
CONECT   19   18   20   53                                                  
CONECT   20   19   21   22   54                                             
CONECT   21   20   55                                                       
CONECT   22   20   23   56   57                                             
CONECT   23   22   24   58   59                                             
CONECT   24   23   25   26   18                                             
CONECT   25   24   60   61   62                                             
CONECT   26   24   27   15   63                                             
CONECT   27   26   28   64   65                                             
CONECT   28   27   29   66   67                                             
CONECT   29   28   30   10   14                                             
CONECT   30   29   68   69   70                                             
CONECT   31    1                                                            
CONECT   32    1                                                            
CONECT   33    1                                                            
CONECT   34    2                                                            
CONECT   35    3                                                            
CONECT   36    3                                                            
CONECT   37    3                                                            
CONECT   38    4                                                            
CONECT   39    5                                                            
CONECT   40    5                                                            
CONECT   41    5                                                            
CONECT   42    6                                                            
CONECT   43    7                                                            
CONECT   44    8                                                            
CONECT   45    9                                                            
CONECT   46    9                                                            
CONECT   47    9                                                            
CONECT   48   10                                                            
CONECT   49   11                                                            
CONECT   50   11                                                            
CONECT   51   16                                                            
CONECT   52   17                                                            
CONECT   53   19                                                            
CONECT   54   20                                                            
CONECT   55   21                                                            
CONECT   56   22                                                            
CONECT   57   22                                                            
CONECT   58   23                                                            
CONECT   59   23                                                            
CONECT   60   25                                                            
CONECT   61   25                                                            
CONECT   62   25                                                            
CONECT   63   26                                                            
CONECT   64   27                                                            
CONECT   65   27                                                            
CONECT   66   28                                                            
CONECT   67   28                                                            
CONECT   68   30                                                            
CONECT   69   30                                                            
CONECT   70   30                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  146    0
END

RDKit          3D

70 73  0  0  0  0  0  0  0  0999 V2000
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    0.9330    0.0710    0.3690 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2477    1.4773   -0.2802 C   0  0  0  0  0  0  0  0  0  0  0  0
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  9 47  1  0
 10 48  1  1
 11 49  1  0
 11 50  1  0
 16 51  1  0
 17 52  1  0
 19 53  1  0
 20 54  1  1
 21 55  1  0
 22 56  1  0
 22 57  1  0
 23 58  1  0
 23 59  1  0
 25 60  1  0
 25 61  1  0
 25 62  1  0
 26 63  1  1
 27 64  1  0
 27 65  1  0
 28 66  1  0
 28 67  1  0
 30 68  1  0
 30 69  1  0
 30 70  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₂₈H₄₀O₂

Average Mass

408.6260 Da

Monoisotopic Mass

408.30283 Da

IUPAC Name

(1R,2R,5S,14R,15R)-14-[(2R,3E,5R)-5,6-dimethylhept-3-en-2-yl]-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-6,8,10-trien-12-one

Traditional Name

(1R,2R,5S,14R,15R)-14-[(2R,3E,5R)-5,6-dimethylhept-3-en-2-yl]-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-6,8,10-trien-12-one

CAS Registry Number

Not Available

SMILES

[H]\C(=C(\[H])[C@@]([H])(C)[C@@]1([H])CC(=O)C2=C3C=CC4=C[C@@]([H])(O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@]([H])(C)C(C)C

InChI Identifier

InChI=1S/C28H40O2/c1-17(2)18(3)7-8-19(4)24-16-25(30)26-22-10-9-20-15-21(29)11-13-27(20,5)23(22)12-14-28(24,26)6/h7-10,15,17-19,21,23-24,29H,11-14,16H2,1-6H3/b8-7+/t18-,19+,21-,23-,24+,27-,28+/m0/s1

InChI Key

XRXZKBAAJAKIMB-AXOAYYPZSA-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
Gymnascella	NPAtlas	17988094
Gymnoascus dankaliensis	Fungi	KNApSAcK

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	5.72	ALOGPS
logP	5.72	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Acidic)	17.59	ChemAxon
pKa (Strongest Basic)	-1.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	128.52 m³·mol⁻¹	ChemAxon
Polarizability	49.88 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA012199

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00039313

Chemspider ID

23076737

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24179451

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Gymnasterone C (NP0007406)

MOL for NP0007406 (Gymnasterone C)

3D MOL for NP0007406 (Gymnasterone C)

3D SDF for NP0007406 (Gymnasterone C)

3D-SDF for NP0007406 (Gymnasterone C)

PDB for NP0007406 (Gymnasterone C)

3D PDB for NP0007406 (Gymnasterone C)

SMILES for NP0007406 (Gymnasterone C)

INCHI for NP0007406 (Gymnasterone C)

Structure for NP0007406 (Gymnasterone C)

3D Structure for NP0007406 (Gymnasterone C)