NP-MRD: Showing NP-Card for (8R,8'R,9S)-cubebin (NP0031992)

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Record Information

Version

2.0

Created at

2021-06-19 22:55:09 UTC

Updated at

2021-08-20 00:00:24 UTC

NP-MRD ID

NP0031992

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(8R,8'R,9S)-cubebin

Provided By

JEOL Database JEOL Logo

Description

(-)-Cubebin is also known as beta-cubebin (-)-cubebin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. (8R,8'R,9S)-cubebin is found in Apis cerana, Aristolochia chamissonis, Aristolochia cymbifera, Aristolochia elegans, Aristolochia lagesiana, Aristolochia pubescens, Aristolochia ringens, Aristolochia tomentosa, Hypenia salzmannii, Justicia hyssopifolia, Piper guineense, Piper ribesioides, Piper trichostachyon, Protium tenuifolium, Virola flexuosa, Virola surinamensis and Zanthoxylum petiolare. (8R,8'R,9S)-cubebin was first documented in 2021 (PMID: 34110481). Based on a literature review very few articles have been published on (-)-cubebin (PMID: 33905595).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202100553D          

 46 50  0  0  0  0            999 V2000
    2.2408   -0.6032    0.5589 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6787    0.5362    1.1827 C   0  0  1  0  0  0  0  0  0  0  0  0
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    1.6787    2.3068   -0.3212 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4694    1.4280   -0.6251 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7364    2.2051   -1.1594 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4743    2.8438   -2.5031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4071    2.0450   -3.6679 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3710    6.0331   -5.5513 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2813    4.7020   -6.1001 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.8838   -1.0843    2.0382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1502   -2.2154    2.4623 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1 27  1  0  0  0  0
M  END

     RDKit          3D

 46 50  0  0  0  0  0  0  0  0999 V2000
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    1.6787    0.5362    1.1827 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652306202100553D          

 46 50  0  0  0  0            999 V2000
    2.2408   -0.6032    0.5589 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6787    0.5362    1.1827 C   0  0  1  0  0  0  0  0  0  0  0  0
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  5  6  1  0  0  0  0
  8 34  1  0  0  0  0
  9 35  1  0  0  0  0
 12 36  1  0  0  0  0
 20 43  1  0  0  0  0
 23 44  1  0  0  0  0
 25 45  1  0  0  0  0
 25 46  1  0  0  0  0
 19 42  1  0  0  0  0
  6 32  1  0  0  0  0
  6 33  1  0  0  0  0
 17 40  1  0  0  0  0
 17 41  1  0  0  0  0
  4 29  1  0  0  0  0
  4 30  1  0  0  0  0
  2 28  1  1  0  0  0
 14 37  1  0  0  0  0
 14 38  1  0  0  0  0
  1 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0031992

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])OC([H])([H])[C@]([H])(C([H])([H])C2=C([H])C3=C(OC([H])([H])O3)C([H])=C2[H])[C@@]1([H])C([H])([H])C1=C([H])C2=C(OC([H])([H])O2)C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C20H20O6/c21-20-15(6-13-2-4-17-19(8-13)26-11-24-17)14(9-22-20)5-12-1-3-16-18(7-12)25-10-23-16/h1-4,7-8,14-15,20-21H,5-6,9-11H2/t14-,15+,20-/m0/s1

> <INCHI_KEY>
DIYWRNLYKJKHAM-MDOVXXIYSA-N

> <FORMULA>
C20H20O6

> <MOLECULAR_WEIGHT>
356.374

> <EXACT_MASS>
356.125988364

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
37.679772605162

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R,4R)-3,4-bis[(2H-1,3-benzodioxol-5-yl)methyl]oxolan-2-ol

> <ALOGPS_LOGP>
2.54

> <JCHEM_LOGP>
3.1849300903333324

> <ALOGPS_LOGS>
-3.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.16554771197489

> <JCHEM_PKA_STRONGEST_BASIC>
-4.038589430782182

> <JCHEM_POLAR_SURFACE_AREA>
66.38000000000001

> <JCHEM_REFRACTIVITY>
91.50760000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.68e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cubebin

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 46 50  0  0  0  0  0  0  0  0999 V2000
    2.2408   -0.6032    0.5589 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6787    0.5362    1.1827 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4156    1.6739    0.7375 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6787    2.3068   -0.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4694    1.4280   -0.6251 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7364    2.2051   -1.1594 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4743    2.8438   -2.5031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4071    2.0450   -3.6679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1541    2.6157   -4.9193 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0267    3.9797   -4.9766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0372    4.7652   -3.8506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2853    4.2314   -2.6033 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1697    6.0814   -4.1234 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3710    6.0331   -5.5513 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2813    4.7020   -6.1001 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2387    0.7669    0.7333 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6351   -0.4877    0.6723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8838   -1.0843    2.0382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1502   -2.2154    2.4623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3531   -2.7720    3.7289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2899   -2.1792    4.5463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0075   -1.0781    4.1439 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8292   -0.5073    2.9013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8763   -0.6477    5.0976 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6269   -1.6092    6.1441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6167   -2.5811    5.8035 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1509   -0.6344    0.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7690    0.4354    2.2688 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3328    2.4263   -1.1904 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3905    3.3019    0.0344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7682    0.6604   -1.3526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6009    1.5383   -1.2653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0429    2.9726   -0.4369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5528    0.9683   -3.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1010    2.0071   -5.8148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3291    4.8784   -1.7336 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3630    6.4400   -5.7792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3860    6.6626   -6.0333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2173    1.5091    1.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6092   -0.2459    0.2291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1968   -1.2427    0.0076 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5884   -2.6638    1.7990 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2069   -3.6398    4.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4100    0.3613    2.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3066   -1.0718    7.0441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5616   -2.1376    6.3646 H   0  0  0  0  0  0  0  0  0  0  0  0
 20 19  2  0
 18 23  2  0
 18 17  1  0
 16 17  1  0
 16  5  1  0
 23 22  1  0
 21 22  2  0
 11 12  1  0
  8  9  2  0
 12  7  2  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2 16  1  0
  6  7  1  0
 11 10  2  0
  7  8  1  0
  9 10  1  0
 22 24  1  0
 24 25  1  0
 25 26  1  0
 10 15  1  0
 15 14  1  0
 14 13  1  0
 13 11  1  0
 26 21  1  0
  2  1  1  0
 18 19  1  0
 16 39  1  1
 21 20  1  0
  5 31  1  6
  5  6  1  0
  8 34  1  0
  9 35  1  0
 12 36  1  0
 20 43  1  0
 23 44  1  0
 25 45  1  0
 25 46  1  0
 19 42  1  0
  6 32  1  0
  6 33  1  0
 17 40  1  0
 17 41  1  0
  4 29  1  0
  4 30  1  0
  2 28  1  1
 14 37  1  0
 14 38  1  0
  1 27  1  0
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  O   UNK     0       2.241  -0.603   0.559  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.679   0.536   1.183  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.416   1.674   0.738  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.679   2.307  -0.321  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.469   1.428  -0.625  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.736   2.205  -1.159  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.474   2.844  -2.503  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.407   2.045  -3.668  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.154   2.616  -4.919  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.027   3.980  -4.977  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.037   4.765  -3.851  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.285   4.231  -2.603  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.170   6.081  -4.123  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.371   6.033  -5.551  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.281   4.702  -6.100  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.239   0.767   0.733  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.635  -0.488   0.672  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.884  -1.084   2.038  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.150  -2.215   2.462  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.353  -2.772   3.729  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.290  -2.179   4.546  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.007  -1.078   4.144  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.829  -0.507   2.901  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.876  -0.648   5.098  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.627  -1.609   6.144  0.00  0.00           C+0
HETATM   26  O   UNK     0      -1.617  -2.581   5.803  0.00  0.00           O+0
HETATM   27  H   UNK     0       3.151  -0.634   0.899  0.00  0.00           H+0
HETATM   28  H   UNK     0       1.769   0.435   2.269  0.00  0.00           H+0
HETATM   29  H   UNK     0       2.333   2.426  -1.190  0.00  0.00           H+0
HETATM   30  H   UNK     0       1.391   3.302   0.034  0.00  0.00           H+0
HETATM   31  H   UNK     0       0.768   0.660  -1.353  0.00  0.00           H+0
HETATM   32  H   UNK     0      -1.601   1.538  -1.265  0.00  0.00           H+0
HETATM   33  H   UNK     0      -1.043   2.973  -0.437  0.00  0.00           H+0
HETATM   34  H   UNK     0      -0.553   0.968  -3.600  0.00  0.00           H+0
HETATM   35  H   UNK     0      -0.101   2.007  -5.815  0.00  0.00           H+0
HETATM   36  H   UNK     0      -0.329   4.878  -1.734  0.00  0.00           H+0
HETATM   37  H   UNK     0       1.363   6.440  -5.779  0.00  0.00           H+0
HETATM   38  H   UNK     0      -0.386   6.663  -6.033  0.00  0.00           H+0
HETATM   39  H   UNK     0      -0.217   1.509   1.404  0.00  0.00           H+0
HETATM   40  H   UNK     0      -1.609  -0.246   0.229  0.00  0.00           H+0
HETATM   41  H   UNK     0      -0.197  -1.243   0.008  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.588  -2.664   1.799  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.207  -3.640   4.058  0.00  0.00           H+0
HETATM   44  H   UNK     0      -2.410   0.361   2.610  0.00  0.00           H+0
HETATM   45  H   UNK     0      -2.307  -1.072   7.044  0.00  0.00           H+0
HETATM   46  H   UNK     0      -3.562  -2.138   6.365  0.00  0.00           H+0
CONECT    1    2   27                                                       
CONECT    2    3   16    1   28                                             
CONECT    3    4    2                                                       
CONECT    4    5    3   29   30                                             
CONECT    5   16    4   31    6                                             
CONECT    6    7    5   32   33                                             
CONECT    7   12    6    8                                                  
CONECT    8    9    7   34                                                  
CONECT    9    8   10   35                                                  
CONECT   10   11    9   15                                                  
CONECT   11   12   10   13                                                  
CONECT   12   11    7   36                                                  
CONECT   13   14   11                                                       
CONECT   14   15   13   37   38                                             
CONECT   15   10   14                                                       
CONECT   16   17    5    2   39                                             
CONECT   17   18   16   40   41                                             
CONECT   18   23   17   19                                                  
CONECT   19   20   18   42                                                  
CONECT   20   19   21   43                                                  
CONECT   21   22   26   20                                                  
CONECT   22   23   21   24                                                  
CONECT   23   18   22   44                                                  
CONECT   24   22   25                                                       
CONECT   25   24   26   45   46                                             
CONECT   26   25   21                                                       
CONECT   27    1                                                            
CONECT   28    2                                                            
CONECT   29    4                                                            
CONECT   30    4                                                            
CONECT   31    5                                                            
CONECT   32    6                                                            
CONECT   33    6                                                            
CONECT   34    8                                                            
CONECT   35    9                                                            
CONECT   36   12                                                            
CONECT   37   14                                                            
CONECT   38   14                                                            
CONECT   39   16                                                            
CONECT   40   17                                                            
CONECT   41   17                                                            
CONECT   42   19                                                            
CONECT   43   20                                                            
CONECT   44   23                                                            
CONECT   45   25                                                            
CONECT   46   25                                                            
MASTER        0    0    0    0    0    0    0    0   46    0  100    0
END

RDKit          3D

46 50  0  0  0  0  0  0  0  0999 V2000
    2.2408   -0.6032    0.5589 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6787    0.5362    1.1827 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4156    1.6739    0.7375 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6787    2.3068   -0.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4694    1.4280   -0.6251 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7364    2.2051   -1.1594 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4743    2.8438   -2.5031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4071    2.0450   -3.6679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1541    2.6157   -4.9193 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0267    3.9797   -4.9766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0372    4.7652   -3.8506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2853    4.2314   -2.6033 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1697    6.0814   -4.1234 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3710    6.0331   -5.5513 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2813    4.7020   -6.1001 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2387    0.7669    0.7333 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6351   -0.4877    0.6723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8838   -1.0843    2.0382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1502   -2.2154    2.4623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3531   -2.7720    3.7289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2899   -2.1792    4.5463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0075   -1.0781    4.1439 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8292   -0.5073    2.9013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8763   -0.6477    5.0976 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6269   -1.6092    6.1441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6167   -2.5811    5.8035 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1509   -0.6344    0.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7690    0.4354    2.2688 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3328    2.4263   -1.1904 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3905    3.3019    0.0344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7682    0.6604   -1.3526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6009    1.5383   -1.2653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0429    2.9726   -0.4369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5528    0.9683   -3.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1010    2.0071   -5.8148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3291    4.8784   -1.7336 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3630    6.4400   -5.7792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3860    6.6626   -6.0333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2173    1.5091    1.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6092   -0.2459    0.2291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1968   -1.2427    0.0076 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5884   -2.6638    1.7990 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2069   -3.6398    4.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4100    0.3613    2.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3066   -1.0718    7.0441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5616   -2.1376    6.3646 H   0  0  0  0  0  0  0  0  0  0  0  0
 20 19  2  0
 18 23  2  0
 18 17  1  0
 16 17  1  0
 16  5  1  0
 23 22  1  0
 21 22  2  0
 11 12  1  0
  8  9  2  0
 12  7  2  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2 16  1  0
  6  7  1  0
 11 10  2  0
  7  8  1  0
  9 10  1  0
 22 24  1  0
 24 25  1  0
 25 26  1  0
 10 15  1  0
 15 14  1  0
 14 13  1  0
 13 11  1  0
 26 21  1  0
  2  1  1  0
 18 19  1  0
 16 39  1  1
 21 20  1  0
  5 31  1  6
  5  6  1  0
  8 34  1  0
  9 35  1  0
 12 36  1  0
 20 43  1  0
 23 44  1  0
 25 45  1  0
 25 46  1  0
 19 42  1  0
  6 32  1  0
  6 33  1  0
 17 40  1  0
 17 41  1  0
  4 29  1  0
  4 30  1  0
  2 28  1  1
 14 37  1  0
 14 38  1  0
  1 27  1  0
M  END

View in JSmol View DFT Assignments 3D Conformers

Synonyms

Value	Source
(8R,8'r,9S)-Cubebin	ChEBI
3,4-Bis(2H-1,3-benzodioxol-5-ylmethyl)oxolan-2-ol	ChEBI
9-Hydroxy-3,4:3',4'-bis(methylenedioxy)-9,9'-epoxylignan	ChEBI
beta-Cubebin	ChEBI
b-Cubebin	Generator
Β-cubebin	Generator

Chemical Formula

C₂₀H₂₀O₆

Average Mass

356.3740 Da

Monoisotopic Mass

356.12599 Da

IUPAC Name

(2S,3R,4R)-3,4-bis[(2H-1,3-benzodioxol-5-yl)methyl]oxolan-2-ol

Traditional Name

cubebin

CAS Registry Number

Not Available

SMILES

[H]O[C@@]1([H])OC([H])([H])[C@]([H])(C([H])([H])C2=C([H])C3=C(OC([H])([H])O3)C([H])=C2[H])[C@@]1([H])C([H])([H])C1=C([H])C2=C(OC([H])([H])O2)C([H])=C1[H]

InChI Identifier

InChI=1S/C20H20O6/c21-20-15(6-13-2-4-17-19(8-13)26-11-24-17)14(9-22-20)5-12-1-3-16-18(7-12)25-10-23-16/h1-4,7-8,14-15,20-21H,5-6,9-11H2/t14-,15+,20-/m0/s1

InChI Key

DIYWRNLYKJKHAM-MDOVXXIYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 150 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 175 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 225 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 250 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, chcl3, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, chcl3, 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
Abies sachalinensis	KNApSAcK Database	22123792
Apis cerana	LOTUS Database	35616633
Araucaria angustifolia	KNApSAcK Database	22123792
Aristolochia chamissonis	LOTUS Database	35616633
Aristolochia cymbifera	LOTUS Database	35616633
Aristolochia elegans	LOTUS Database	35616633
Aristolochia lagesiana	JEOL database	Pascoli, I. C., et al, Phytochemistry 67, 735 (2006)
Aristolochia pubescens	JEOL database	Pascoli, I. C., et al, Phytochemistry 67, 735 (2006)
Aristolochia ringens	LOTUS Database	35616633
Aristolochia tomentosa	LOTUS Database	35616633
Aristolochia triangularis	KNApSAcK Database	22123792
Bauhinia tarapotensis	KNApSAcK Database	22123792
Betula pendula	KNApSAcK Database	22123792
Coptis japonica var. dissecta	KNApSAcK Database	22123792
Cryptomeria japonica	KNApSAcK Database	22123792
Cynomorium songaricum	KNApSAcK Database	22123792
Fagraea racemosa	KNApSAcK Database	22123792
Fitzroya cupressoides	KNApSAcK Database	22123792
Gaultheria yunnanensis	KNApSAcK Database	22123792
Hedyotis chrysotricha	KNApSAcK Database	22123792
Heritiera littoralis	KNApSAcK Database	22123792
Hypenia salzmannii	LOTUS Database	35616633
Isatis indigotica	KNApSAcK Database	22123792
Justicia diffusa var. prostrata	KNApSAcK Database	22123792
Justicia flava	KNApSAcK Database	22123792
Justicia glauca	KNApSAcK Database	22123792
Justicia hyssopifolia	LOTUS Database	35616633
Justicia tranquebariensis	KNApSAcK Database	22123792
Larix dahurica	KNApSAcK Database	22123792
Larix leptolepis	KNApSAcK Database	22123792
Larix sibirica	KNApSAcK Database	22123792
Lychnophora ericoides	KNApSAcK Database	22123792
Melodinus morsei	KNApSAcK Database	22123792
Picea excelsa	KNApSAcK Database	22123792
Pinus massoniana	KNApSAcK Database	22123792
Pinus sylvestris	KNApSAcK Database	22123792
Piper cubeba	KNApSAcK Database	22123792
Piper guineense	LOTUS Database	35616633
Piper nigrum	KNApSAcK Database	22123792
Piper ribesioides	LOTUS Database	35616633
Piper trichostachyon	LOTUS Database	35616633
Protium tenuifolium	LOTUS Database	35616633
Reseda suffruticosa	KNApSAcK Database	22123792
Rubia akane	KNApSAcK Database	22123792
Schisandra nigra	KNApSAcK Database	22123792
Symplocos lancifolia	KNApSAcK Database	22123792
Taxus baccata	KNApSAcK Database	22123792
Taxus cuspidata	KNApSAcK Database	22123792
Taxus mairei	KNApSAcK Database	22123792
Tinospora smilacina	KNApSAcK Database	22123792
Ulmus davidiana var. japonica	KNApSAcK Database	22123792
Urtica dioica	KNApSAcK Database	22123792
Virola flexuosa	LOTUS Database	35616633
Virola surinamensis	LOTUS Database	35616633
Wikstroemia glabra	KNApSAcK Database	22123792
Zanthoxylum naranjillo	KNApSAcK Database	22123792
Zanthoxylum petiolare	LOTUS Database	35616633

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	131.50 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Boiling Point	526.80 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	11 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	3.340 (est)	The Good Scents Company Information System

Predicted Properties

Property	Value	Source
logP	2.54	ALOGPS
logP	3.18	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	12.17	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	66.38 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	91.51 m³·mol⁻¹	ChemAxon
Polarizability	37.68 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002591

Chemspider ID

104954

KEGG Compound ID

C10549

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

65684

Good Scents ID

rw1391571

References

General References

de Souza JM, Santos MFC, Pedroso RCN, Pimenta LP, Siqueira KA, Soares MA, Dias GM, Pietro RCLR, Ramos HP, Silva MLA, Pauletti PM, Veneziani RCS, Ambrosio SR, Braun GH, Januario AH: Optimization of (-)-cubebin biotransformation to (-)-hinokinin by the marine fungus Absidia coerulea 3A9. Arch Microbiol. 2021 Sep;203(7):4313-4318. doi: 10.1007/s00203-021-02417-0. Epub 2021 Jun 10. [PubMed:34110481 ]
Neres NBR, Montagnini D, Ferreira DS, Parreira RLT, Orenha RP, Lima TC, Molina EF, Cunha WR, Silva MLA, Esperandim VR: In Vivo and in Silico Trypanocidal Activity Evaluation of (-)-Cubebin Encapsulated in PLGA Microspheres as Potential Treatment in Acute Phase. Chem Biodivers. 2021 Jun;18(6):e2100052. doi: 10.1002/cbdv.202100052. Epub 2021 Apr 27. [PubMed:33905595 ]
Pascoli, I. C., et al. (2006). Pascoli, I. C., et al, Phytochemistry 67, 735 (2006). Phytochem..

Showing NP-Card for (8R,8'R,9S)-cubebin (NP0031992)

MOL for NP0031992 ((8R,8'R,9S)-cubebin)

3D MOL for NP0031992 ((8R,8'R,9S)-cubebin)

3D SDF for NP0031992 ((8R,8'R,9S)-cubebin)

3D-SDF for NP0031992 ((8R,8'R,9S)-cubebin)

PDB for NP0031992 ((8R,8'R,9S)-cubebin)

3D PDB for NP0031992 ((8R,8'R,9S)-cubebin)

SMILES for NP0031992 ((8R,8'R,9S)-cubebin)

INCHI for NP0031992 ((8R,8'R,9S)-cubebin)

Structure for NP0031992 ((8R,8'R,9S)-cubebin)

3D Structure for NP0031992 ((8R,8'R,9S)-cubebin)