NP-MRD: Showing NP-Card for glaucarubinone (NP0035498)

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Record Information

Version

2.0

Created at

2021-06-20 18:55:39 UTC

Updated at

2021-06-30 00:06:30 UTC

NP-MRD ID

NP0035498

Secondary Accession Numbers

None

Natural Product Identification

Common Name

glaucarubinone

Provided By

JEOL Database JEOL Logo

Description

glaucarubinone is found in Ailanthus excelsa , Ailanthus triphylla, Allanthus excelsa, Odyendyea gabonensis, Perriera madagascariensis, Pierreodendron kerstingii Little., Quassia undulata , Quassia simarouba and Simarouba glauca . glaucarubinone was first documented in 2010 (Usami, Y., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202120553D          

 69 73  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306202120553D          

 69 73  0  0  0  0            999 V2000
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    0.3541   -3.0434   -1.1902 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7479   -3.7870   -1.9644 H   0  0  0  0  0  0  0  0  0  0  0  0
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  2  1  1  0  0  0  0
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 30 62  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0035498

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@]1([H])C(=O)C([H])=C(C([H])([H])[H])[C@]2([H])C([H])([H])[C@@]3([H])OC(=O)[C@]([H])(OC(=O)[C@@](O[H])(C([H])([H])[H])C([H])([H])C([H])([H])[H])[C@@]4([H])[C@@]([H])(C([H])([H])[H])[C@@]([H])(O[H])[C@]5(O[H])OC([H])([H])[C@]34[C@@]5([H])[C@@]12C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C25H34O10/c1-6-22(4,31)21(30)35-16-15-11(3)17(27)25(32)20-23(5)12(10(2)7-13(26)18(23)28)8-14(34-19(16)29)24(15,20)9-33-25/h7,11-12,14-18,20,27-28,31-32H,6,8-9H2,1-5H3/t11-,12+,14-,15-,16-,17-,18-,20-,22-,23-,24+,25+/m1/s1

> <INCHI_KEY>
WRBGCYVAJRRQKP-BIEJVUEESA-N

> <FORMULA>
C25H34O10

> <MOLECULAR_WEIGHT>
494.537

> <EXACT_MASS>
494.215197295

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
49.74674544855323

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4R,5R,6R,7S,8R,11R,13S,17S,18S,19R)-4,5,17-trihydroxy-6,14,18-trimethyl-9,16-dioxo-3,10-dioxapentacyclo[9.8.0.0^{1,7}.0^{4,19}.0^{13,18}]nonadec-14-en-8-yl (2R)-2-hydroxy-2-methylbutanoate

> <ALOGPS_LOGP>
0.32

> <JCHEM_LOGP>
0.3712398596666653

> <ALOGPS_LOGS>
-2.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.426739362741941

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.884471825007157

> <JCHEM_PKA_STRONGEST_BASIC>
-3.655986878952845

> <JCHEM_POLAR_SURFACE_AREA>
159.82

> <JCHEM_REFRACTIVITY>
118.95620000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.25e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4R,5R,6R,7S,8R,11R,13S,17S,18S,19R)-4,5,17-trihydroxy-6,14,18-trimethyl-9,16-dioxo-3,10-dioxapentacyclo[9.8.0.0^{1,7}.0^{4,19}.0^{13,18}]nonadec-14-en-8-yl (2R)-2-hydroxy-2-methylbutanoate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 69 73  0  0  0  0  0  0  0  0999 V2000
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    0.3938    0.8834    0.8463 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8889    3.6585   -2.1198 C   0  0  1  0  0  0  0  0  0  0  0  0
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    1.8926   -3.2125   -0.3052 H   0  0  0  0  0  0  0  0  0  0  0  0
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 26 13  1  0
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M  END

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0      -1.696  -1.342   4.151  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.748  -2.374   3.548  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.180  -2.888   2.163  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.337  -4.097   1.756  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.535  -3.353   2.241  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.066  -1.766   1.110  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.046  -1.180   0.659  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.228  -1.487   0.780  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.404  -0.338  -0.073  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.394   0.883   0.846  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.024   0.879   1.999  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.806   2.035   0.271  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.013   2.064  -0.523  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.049   3.472  -1.123  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.889   3.659  -2.120  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.617   5.100  -2.550  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.034   6.224  -1.639  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.049   5.383  -3.683  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.526   4.301  -4.573  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.120   4.576  -5.616  0.00  0.00           O+0
HETATM   21  C   UNK     0      -0.285   2.848  -4.153  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.283   2.013  -5.308  0.00  0.00           O+0
HETATM   23  C   UNK     0       1.034   2.671  -3.334  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.236   3.072  -4.240  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.124   1.169  -2.789  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.053   0.948  -1.562  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.423   0.822  -2.252  0.00  0.00           C+0
HETATM   28  O   UNK     0       3.169   0.271  -3.557  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.749   0.085  -3.704  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.376   0.103  -5.064  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.366  -1.339  -3.196  0.00  0.00           C+0
HETATM   32  O   UNK     0      -0.060  -1.484  -3.196  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.921  -1.635  -1.796  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.442  -2.990  -1.277  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.744  -0.422  -0.828  0.00  0.00           C+0
HETATM   36  H   UNK     0      -2.687  -1.770   4.332  0.00  0.00           H+0
HETATM   37  H   UNK     0      -1.813  -0.471   3.502  0.00  0.00           H+0
HETATM   38  H   UNK     0      -1.306  -0.994   5.113  0.00  0.00           H+0
HETATM   39  H   UNK     0       0.259  -1.944   3.495  0.00  0.00           H+0
HETATM   40  H   UNK     0      -0.701  -3.217   4.249  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.734  -3.873   1.763  0.00  0.00           H+0
HETATM   42  H   UNK     0      -0.515  -4.943   2.430  0.00  0.00           H+0
HETATM   43  H   UNK     0      -0.609  -4.438   0.750  0.00  0.00           H+0
HETATM   44  H   UNK     0      -3.102  -2.586   2.021  0.00  0.00           H+0
HETATM   45  H   UNK     0      -0.430  -0.253  -0.777  0.00  0.00           H+0
HETATM   46  H   UNK     0       2.853   1.964   0.176  0.00  0.00           H+0
HETATM   47  H   UNK     0       1.942   4.182  -0.294  0.00  0.00           H+0
HETATM   48  H   UNK     0       3.017   3.685  -1.587  0.00  0.00           H+0
HETATM   49  H   UNK     0      -0.029   3.377  -1.580  0.00  0.00           H+0
HETATM   50  H   UNK     0       0.590   6.095  -0.646  0.00  0.00           H+0
HETATM   51  H   UNK     0       2.124   6.257  -1.542  0.00  0.00           H+0
HETATM   52  H   UNK     0       0.711   7.201  -2.015  0.00  0.00           H+0
HETATM   53  H   UNK     0      -0.278   6.394  -4.004  0.00  0.00           H+0
HETATM   54  H   UNK     0      -1.152   2.552  -3.549  0.00  0.00           H+0
HETATM   55  H   UNK     0      -0.924   2.422  -5.931  0.00  0.00           H+0
HETATM   56  H   UNK     0       2.111   4.064  -4.686  0.00  0.00           H+0
HETATM   57  H   UNK     0       3.180   3.120  -3.699  0.00  0.00           H+0
HETATM   58  H   UNK     0       2.374   2.391  -5.082  0.00  0.00           H+0
HETATM   59  H   UNK     0       0.094   0.899  -2.535  0.00  0.00           H+0
HETATM   60  H   UNK     0       4.118   0.168  -1.715  0.00  0.00           H+0
HETATM   61  H   UNK     0       3.947   1.771  -2.375  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.823   0.889  -5.241  0.00  0.00           H+0
HETATM   63  H   UNK     0       1.761  -2.092  -3.891  0.00  0.00           H+0
HETATM   64  H   UNK     0      -0.326  -1.365  -4.130  0.00  0.00           H+0
HETATM   65  H   UNK     0       3.006  -1.764  -1.920  0.00  0.00           H+0
HETATM   66  H   UNK     0       0.354  -3.043  -1.190  0.00  0.00           H+0
HETATM   67  H   UNK     0       1.748  -3.787  -1.964  0.00  0.00           H+0
HETATM   68  H   UNK     0       1.893  -3.212  -0.305  0.00  0.00           H+0
HETATM   69  H   UNK     0       2.517  -0.561  -0.054  0.00  0.00           H+0
CONECT    1    2   36   37   38                                             
CONECT    2    3    1   39   40                                             
CONECT    3    6    5    4    2                                             
CONECT    4    3   41   42   43                                             
CONECT    5    3   44                                                       
CONECT    6    8    7    3                                                  
CONECT    7    6                                                            
CONECT    8    9    6                                                       
CONECT    9   10    8   35   45                                             
CONECT   10   11   12    9                                                  
CONECT   11   10                                                            
CONECT   12   13   10                                                       
CONECT   13   26   12   46   14                                             
CONECT   14   15   13   47   48                                             
CONECT   15   16   49   23   14                                             
CONECT   16   18   17   15                                                  
CONECT   17   16   50   51   52                                             
CONECT   18   16   19   53                                                  
CONECT   19   20   18   21                                                  
CONECT   20   19                                                            
CONECT   21   23   22   19   54                                             
CONECT   22   21   55                                                       
CONECT   23   21   15   24   25                                             
CONECT   24   23   56   57   58                                             
CONECT   25   26   23   29   59                                             
CONECT   26   13   25   27   35                                             
CONECT   27   26   28   60   61                                             
CONECT   28   29   27                                                       
CONECT   29   28   25   31   30                                             
CONECT   30   29   62                                                       
CONECT   31   32   33   29   63                                             
CONECT   32   31   64                                                       
CONECT   33   34   35   31   65                                             
CONECT   34   33   66   67   68                                             
CONECT   35    9   69   26   33                                             
CONECT   36    1                                                            
CONECT   37    1                                                            
CONECT   38    1                                                            
CONECT   39    2                                                            
CONECT   40    2                                                            
CONECT   41    4                                                            
CONECT   42    4                                                            
CONECT   43    4                                                            
CONECT   44    5                                                            
CONECT   45    9                                                            
CONECT   46   13                                                            
CONECT   47   14                                                            
CONECT   48   14                                                            
CONECT   49   15                                                            
CONECT   50   17                                                            
CONECT   51   17                                                            
CONECT   52   17                                                            
CONECT   53   18                                                            
CONECT   54   21                                                            
CONECT   55   22                                                            
CONECT   56   24                                                            
CONECT   57   24                                                            
CONECT   58   24                                                            
CONECT   59   25                                                            
CONECT   60   27                                                            
CONECT   61   27                                                            
CONECT   62   30                                                            
CONECT   63   31                                                            
CONECT   64   32                                                            
CONECT   65   33                                                            
CONECT   66   34                                                            
CONECT   67   34                                                            
CONECT   68   34                                                            
CONECT   69   35                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  146    0
END

RDKit          3D

69 73  0  0  0  0  0  0  0  0999 V2000
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 27 61  1  0
  5 44  1  0
  4 41  1  0
  4 42  1  0
  4 43  1  0
  2 39  1  0
  2 40  1  0
  1 36  1  0
  1 37  1  0
  1 38  1  0
 30 62  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₄O₁₀

Average Mass

494.5370 Da

Monoisotopic Mass

494.21520 Da

IUPAC Name

(1S,4R,5R,6R,7S,8R,11R,13S,17S,18S,19R)-4,5,17-trihydroxy-6,14,18-trimethyl-9,16-dioxo-3,10-dioxapentacyclo[9.8.0.0^{1,7}.0^{4,19}.0^{13,18}]nonadec-14-en-8-yl (2R)-2-hydroxy-2-methylbutanoate

Traditional Name

(1S,4R,5R,6R,7S,8R,11R,13S,17S,18S,19R)-4,5,17-trihydroxy-6,14,18-trimethyl-9,16-dioxo-3,10-dioxapentacyclo[9.8.0.0^{1,7}.0^{4,19}.0^{13,18}]nonadec-14-en-8-yl (2R)-2-hydroxy-2-methylbutanoate

CAS Registry Number

Not Available

SMILES

[H]O[C@]1([H])C(=O)C([H])=C(C([H])([H])[H])[C@]2([H])C([H])([H])[C@@]3([H])OC(=O)[C@]([H])(OC(=O)[C@@](O[H])(C([H])([H])[H])C([H])([H])C([H])([H])[H])[C@@]4([H])[C@@]([H])(C([H])([H])[H])[C@@]([H])(O[H])[C@]5(O[H])OC([H])([H])[C@]34[C@@]5([H])[C@@]12C([H])([H])[H]

InChI Identifier

InChI=1S/C25H34O10/c1-6-22(4,31)21(30)35-16-15-11(3)17(27)25(32)20-23(5)12(10(2)7-13(26)18(23)28)8-14(34-19(16)29)24(15,20)9-33-25/h7,11-12,14-18,20,27-28,31-32H,6,8-9H2,1-5H3/t11-,12+,14-,15-,16-,17-,18-,20-,22-,23-,24+,25+/m1/s1

InChI Key

WRBGCYVAJRRQKP-BIEJVUEESA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, C₅D₅N, 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
Ailanthus excelsa	Plant	KNApSAcK
Ailanthus triphylla	Plant	KNApSAcK
Allanthus excelsa	Plant	KNApSAcK
Odyendyea gabonensis	JEOL database	Usami, Y., et al, J. Nat. Prod. 73, 1553 (2010)
Perriera madagascariensis	Plant	KNApSAcK
Pierreodendron kerstingii Little.	Plant	KNApSAcK
Quassia undulata	Plant	KNApSAcK
Simarouba amara	Plant	KNApSAcK
Simarouba glauca	-	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	0.32	ALOGPS
logP	0.37	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	10.88	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	159.82 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	118.96 m³·mol⁻¹	ChemAxon
Polarizability	49.75 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Usami, Y., et al. (2010). Usami, Y., et al, J. Nat. Prod. 73, 1553 (2010). J. Nat. Prod..

Showing NP-Card for glaucarubinone (NP0035498)

MOL for NP0035498 (glaucarubinone)

3D MOL for NP0035498 (glaucarubinone)

3D SDF for NP0035498 (glaucarubinone)

3D-SDF for NP0035498 (glaucarubinone)

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3D PDB for NP0035498 (glaucarubinone)

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INCHI for NP0035498 (glaucarubinone)

Structure for NP0035498 (glaucarubinone)

3D Structure for NP0035498 (glaucarubinone)