NP-MRD: Showing NP-Card for pavidolide B (NP0041812)

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Record Information

Version

2.0

Created at

2021-06-20 23:38:00 UTC

Updated at

2021-06-30 00:16:33 UTC

NP-MRD ID

NP0041812

Secondary Accession Numbers

None

Natural Product Identification

Common Name

pavidolide B

Provided By

JEOL Database JEOL Logo

Description

Pavidolide B belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. pavidolide B is found in Sinularia pavida. pavidolide B was first documented in 2017 (PMID: 28870073). Based on a literature review a small amount of articles have been published on Pavidolide B (PMID: 31749362) (PMID: 31251629) (PMID: 30908860).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306212101383D          

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M  END

     RDKit          3D

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 23 21  1  0  0  0  0
 15 14  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 14 12  1  0  0  0  0
 21 22  2  0  0  0  0
  6 23  1  0  0  0  0
 15 16  1  0  0  0  0
 23 24  1  0  0  0  0
  7 30  1  1  0  0  0
  7  6  1  0  0  0  0
  6 29  1  6  0  0  0
 10  7  1  0  0  0  0
 23 49  1  6  0  0  0
  6  4  1  0  0  0  0
 19 48  1  6  0  0  0
 10 24  1  0  0  0  0
 24 50  1  6  0  0  0
  7  8  1  0  0  0  0
 10 11  1  6  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  2  0  0  0  0
 10 12  1  0  0  0  0
 16 17  1  0  0  0  0
  8  9  1  0  0  0  0
 16 18  1  0  0  0  0
 24 19  1  0  0  0  0
 12 13  2  0  0  0  0
 15 40  1  6  0  0  0
 14 38  1  0  0  0  0
 14 39  1  0  0  0  0
  8 31  1  0  0  0  0
  8 32  1  0  0  0  0
  3 28  1  0  0  0  0
  9 33  1  0  0  0  0
  9 34  1  0  0  0  0
 16 41  1  1  0  0  0
 11 35  1  0  0  0  0
 11 36  1  0  0  0  0
 11 37  1  0  0  0  0
  1 25  1  0  0  0  0
  1 26  1  0  0  0  0
  1 27  1  0  0  0  0
 17 42  1  0  0  0  0
 17 43  1  0  0  0  0
 17 44  1  0  0  0  0
 18 45  1  0  0  0  0
 18 46  1  0  0  0  0
 18 47  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0041812

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]C1=C(C([H])([H])[H])C([H])([H])C([H])([H])[C@@]2([H])[C@@]([H])(C1=O)[C@]1([H])C(=O)O[C@@]3([H])[C@]1([H])[C@@]2(C(=O)C([H])([H])[C@@]3([H])C([H])(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O4/c1-9(2)11-8-14(22)20(4)12-6-5-10(3)7-13(21)15(12)16-17(20)18(11)24-19(16)23/h7,9,11-12,15-18H,5-6,8H2,1-4H3/t11-,12-,15-,16-,17+,18+,20-/m0/s1

> <INCHI_KEY>
MPNQGWWVAITNMP-OVQIZMNKSA-N

> <FORMULA>
C20H26O4

> <MOLECULAR_WEIGHT>
330.424

> <EXACT_MASS>
330.183109317

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
36.32191370929874

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,8R,9R,12R,13S,16S)-1,5-dimethyl-13-(propan-2-yl)-11-oxatetracyclo[7.6.1.0^{2,8}.0^{12,16}]hexadec-5-ene-7,10,15-trione

> <ALOGPS_LOGP>
2.04

> <JCHEM_LOGP>
3.2920206353333334

> <ALOGPS_LOGS>
-3.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.97635540020278

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.305567261852822

> <JCHEM_PKA_STRONGEST_BASIC>
-4.572436758905152

> <JCHEM_POLAR_SURFACE_AREA>
60.440000000000005

> <JCHEM_REFRACTIVITY>
89.7723

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.11e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,8R,9R,12R,13S,16S)-13-isopropyl-1,5-dimethyl-11-oxatetracyclo[7.6.1.0^{2,8}.0^{12,16}]hexadec-5-ene-7,10,15-trione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 50 53  0  0  0  0  0  0  0  0999 V2000
   -1.1905    1.7742   -5.3250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6251    0.9143   -4.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2796   -0.3598   -4.4846 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1934   -1.3436   -3.4769 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9747   -2.2268   -3.8232 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3626   -1.2442   -2.0682 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3145   -0.1577   -1.2315 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6721    1.1209   -2.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4619    1.6344   -2.8969 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4843   -0.8570   -0.4509 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8911   -0.5283   -0.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4549   -0.3648    1.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2636    0.8296    1.2529 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7264   -1.3163    2.1441 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9990   -2.7722    1.7520 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9094   -3.7049    3.0022 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2134   -5.1697    2.6617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8646   -3.2610    4.1192 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0438   -3.1943    0.6329 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3235   -3.0050    1.0069 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0540   -2.6856   -0.1044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2646   -2.5476   -0.1159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1341   -2.5242   -1.2844 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2242   -2.3756   -0.6242 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1715    2.1635   -5.0333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5251    2.6195   -5.5286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3196    1.2196   -6.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3501   -0.7699   -5.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4395   -1.0510   -2.1592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4443    0.1441   -0.4921 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5684    0.9850   -2.6168 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9194    1.9030   -1.2722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4169    1.6332   -2.3581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2304    2.6859   -3.1134 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1359    0.5324   -0.8525 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9930   -0.7802   -2.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6554   -1.0923   -0.4306 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8548   -1.2623    2.8082 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5915   -0.9150    2.6845 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0229   -2.8362    1.3576 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8888   -3.6635    3.4049 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2573   -5.7816    3.5695 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4347   -5.6061    2.0297 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1738   -5.2649    2.1442 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5860   -2.2823    4.5211 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8967   -3.2042    3.7572 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8392   -3.9652    4.9582 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1734   -4.2537    0.3857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2019   -3.4375   -1.8861 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0052   -2.8211   -1.2534 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0
  9  2  1  0
 19 15  1  0
 23 21  1  0
 15 14  1  0
 19 20  1  0
 21 20  1  0
 14 12  1  0
 21 22  2  0
  6 23  1  0
 15 16  1  0
 23 24  1  0
  7 30  1  1
  7  6  1  0
  6 29  1  6
 10  7  1  0
 23 49  1  6
  6  4  1  0
 19 48  1  6
 10 24  1  0
 24 50  1  6
  7  8  1  0
 10 11  1  6
  2  1  1  0
  4  3  1  0
  4  5  2  0
 10 12  1  0
 16 17  1  0
  8  9  1  0
 16 18  1  0
 24 19  1  0
 12 13  2  0
 15 40  1  6
 14 38  1  0
 14 39  1  0
  8 31  1  0
  8 32  1  0
  3 28  1  0
  9 33  1  0
  9 34  1  0
 16 41  1  1
 11 35  1  0
 11 36  1  0
 11 37  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
 17 42  1  0
 17 43  1  0
 17 44  1  0
 18 45  1  0
 18 46  1  0
 18 47  1  0
M  END

HEADER    PROTEIN                                 21-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JUN-21         0                                  
HETATM    1  C   UNK     0      -1.190   1.774  -5.325  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.625   0.914  -4.222  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.280  -0.360  -4.485  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.193  -1.344  -3.477  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.975  -2.227  -3.823  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.363  -1.244  -2.068  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.315  -0.158  -1.232  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.672   1.121  -2.001  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.462   1.634  -2.897  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.484  -0.857  -0.451  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.891  -0.528  -0.978  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.455  -0.365   1.002  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.264   0.830   1.253  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.726  -1.316   2.144  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.999  -2.772   1.752  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.909  -3.705   3.002  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.213  -5.170   2.662  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.865  -3.261   4.119  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.044  -3.194   0.633  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.324  -3.005   1.007  0.00  0.00           O+0
HETATM   21  C   UNK     0      -1.054  -2.686  -0.104  0.00  0.00           C+0
HETATM   22  O   UNK     0      -2.265  -2.548  -0.116  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.134  -2.524  -1.284  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.224  -2.376  -0.624  0.00  0.00           C+0
HETATM   25  H   UNK     0      -2.172   2.163  -5.033  0.00  0.00           H+0
HETATM   26  H   UNK     0      -0.525   2.619  -5.529  0.00  0.00           H+0
HETATM   27  H   UNK     0      -1.320   1.220  -6.261  0.00  0.00           H+0
HETATM   28  H   UNK     0      -0.350  -0.770  -5.488  0.00  0.00           H+0
HETATM   29  H   UNK     0      -1.440  -1.051  -2.159  0.00  0.00           H+0
HETATM   30  H   UNK     0      -0.444   0.144  -0.492  0.00  0.00           H+0
HETATM   31  H   UNK     0       1.568   0.985  -2.617  0.00  0.00           H+0
HETATM   32  H   UNK     0       0.919   1.903  -1.272  0.00  0.00           H+0
HETATM   33  H   UNK     0      -1.417   1.633  -2.358  0.00  0.00           H+0
HETATM   34  H   UNK     0      -0.230   2.686  -3.113  0.00  0.00           H+0
HETATM   35  H   UNK     0       3.136   0.532  -0.853  0.00  0.00           H+0
HETATM   36  H   UNK     0       2.993  -0.780  -2.039  0.00  0.00           H+0
HETATM   37  H   UNK     0       3.655  -1.092  -0.431  0.00  0.00           H+0
HETATM   38  H   UNK     0       0.855  -1.262   2.808  0.00  0.00           H+0
HETATM   39  H   UNK     0       2.591  -0.915   2.684  0.00  0.00           H+0
HETATM   40  H   UNK     0       3.023  -2.836   1.358  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.889  -3.664   3.405  0.00  0.00           H+0
HETATM   42  H   UNK     0       2.257  -5.782   3.570  0.00  0.00           H+0
HETATM   43  H   UNK     0       1.435  -5.606   2.030  0.00  0.00           H+0
HETATM   44  H   UNK     0       3.174  -5.265   2.144  0.00  0.00           H+0
HETATM   45  H   UNK     0       2.586  -2.282   4.521  0.00  0.00           H+0
HETATM   46  H   UNK     0       3.897  -3.204   3.757  0.00  0.00           H+0
HETATM   47  H   UNK     0       2.839  -3.965   4.958  0.00  0.00           H+0
HETATM   48  H   UNK     0       1.173  -4.254   0.386  0.00  0.00           H+0
HETATM   49  H   UNK     0      -0.202  -3.438  -1.886  0.00  0.00           H+0
HETATM   50  H   UNK     0       2.005  -2.821  -1.253  0.00  0.00           H+0
CONECT    1    2   25   26   27                                             
CONECT    2    3    9    1                                                  
CONECT    3    2    4   28                                                  
CONECT    4    6    3    5                                                  
CONECT    5    4                                                            
CONECT    6   23    7   29    4                                             
CONECT    7   30    6   10    8                                             
CONECT    8    7    9   31   32                                             
CONECT    9    2    8   33   34                                             
CONECT   10    7   24   11   12                                             
CONECT   11   10   35   36   37                                             
CONECT   12   14   10   13                                                  
CONECT   13   12                                                            
CONECT   14   15   12   38   39                                             
CONECT   15   19   14   16   40                                             
CONECT   16   15   17   18   41                                             
CONECT   17   16   42   43   44                                             
CONECT   18   16   45   46   47                                             
CONECT   19   15   20   48   24                                             
CONECT   20   19   21                                                       
CONECT   21   23   20   22                                                  
CONECT   22   21                                                            
CONECT   23   21    6   24   49                                             
CONECT   24   23   10   50   19                                             
CONECT   25    1                                                            
CONECT   26    1                                                            
CONECT   27    1                                                            
CONECT   28    3                                                            
CONECT   29    6                                                            
CONECT   30    7                                                            
CONECT   31    8                                                            
CONECT   32    8                                                            
CONECT   33    9                                                            
CONECT   34    9                                                            
CONECT   35   11                                                            
CONECT   36   11                                                            
CONECT   37   11                                                            
CONECT   38   14                                                            
CONECT   39   14                                                            
CONECT   40   15                                                            
CONECT   41   16                                                            
CONECT   42   17                                                            
CONECT   43   17                                                            
CONECT   44   17                                                            
CONECT   45   18                                                            
CONECT   46   18                                                            
CONECT   47   18                                                            
CONECT   48   19                                                            
CONECT   49   23                                                            
CONECT   50   24                                                            
MASTER        0    0    0    0    0    0    0    0   50    0  106    0
END

RDKit          3D

50 53  0  0  0  0  0  0  0  0999 V2000
   -1.1905    1.7742   -5.3250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6251    0.9143   -4.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2796   -0.3598   -4.4846 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1934   -1.3436   -3.4769 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9747   -2.2268   -3.8232 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3626   -1.2442   -2.0682 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3145   -0.1577   -1.2315 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6721    1.1209   -2.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4619    1.6344   -2.8969 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4843   -0.8570   -0.4509 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8911   -0.5283   -0.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4549   -0.3648    1.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2636    0.8296    1.2529 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7264   -1.3163    2.1441 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9990   -2.7722    1.7520 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9094   -3.7049    3.0022 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2134   -5.1697    2.6617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8646   -3.2610    4.1192 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0438   -3.1943    0.6329 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3235   -3.0050    1.0069 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0540   -2.6856   -0.1044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2646   -2.5476   -0.1159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1341   -2.5242   -1.2844 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2242   -2.3756   -0.6242 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1715    2.1635   -5.0333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5251    2.6195   -5.5286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3196    1.2196   -6.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3501   -0.7699   -5.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4395   -1.0510   -2.1592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4443    0.1441   -0.4921 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5684    0.9850   -2.6168 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9194    1.9030   -1.2722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4169    1.6332   -2.3581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2304    2.6859   -3.1134 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1359    0.5324   -0.8525 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9930   -0.7802   -2.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6554   -1.0923   -0.4306 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8548   -1.2623    2.8082 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5915   -0.9150    2.6845 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0229   -2.8362    1.3576 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8888   -3.6635    3.4049 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2573   -5.7816    3.5695 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4347   -5.6061    2.0297 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1738   -5.2649    2.1442 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5860   -2.2823    4.5211 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8967   -3.2042    3.7572 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8392   -3.9652    4.9582 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1734   -4.2537    0.3857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2019   -3.4375   -1.8861 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0052   -2.8211   -1.2534 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0
  9  2  1  0
 19 15  1  0
 23 21  1  0
 15 14  1  0
 19 20  1  0
 21 20  1  0
 14 12  1  0
 21 22  2  0
  6 23  1  0
 15 16  1  0
 23 24  1  0
  7 30  1  1
  7  6  1  0
  6 29  1  6
 10  7  1  0
 23 49  1  6
  6  4  1  0
 19 48  1  6
 10 24  1  0
 24 50  1  6
  7  8  1  0
 10 11  1  6
  2  1  1  0
  4  3  1  0
  4  5  2  0
 10 12  1  0
 16 17  1  0
  8  9  1  0
 16 18  1  0
 24 19  1  0
 12 13  2  0
 15 40  1  6
 14 38  1  0
 14 39  1  0
  8 31  1  0
  8 32  1  0
  3 28  1  0
  9 33  1  0
  9 34  1  0
 16 41  1  1
 11 35  1  0
 11 36  1  0
 11 37  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
 17 42  1  0
 17 43  1  0
 17 44  1  0
 18 45  1  0
 18 46  1  0
 18 47  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₆O₄

Average Mass

330.4240 Da

Monoisotopic Mass

330.18311 Da

IUPAC Name

(1R,2S,8R,9R,12R,13S,16S)-1,5-dimethyl-13-(propan-2-yl)-11-oxatetracyclo[7.6.1.0^{2,8}.0^{12,16}]hexadec-5-ene-7,10,15-trione

Traditional Name

(1R,2S,8R,9R,12R,13S,16S)-13-isopropyl-1,5-dimethyl-11-oxatetracyclo[7.6.1.0^{2,8}.0^{12,16}]hexadec-5-ene-7,10,15-trione

CAS Registry Number

Not Available

SMILES

[H]C1=C(C([H])([H])[H])C([H])([H])C([H])([H])[C@@]2([H])[C@@]([H])(C1=O)[C@]1([H])C(=O)O[C@@]3([H])[C@]1([H])[C@@]2(C(=O)C([H])([H])[C@@]3([H])C([H])(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]

InChI Identifier

InChI=1S/C20H26O4/c1-9(2)11-8-14(22)20(4)12-6-5-10(3)7-13(21)15(12)16-17(20)18(11)24-19(16)23/h7,9,11-12,15-18H,5-6,8H2,1-4H3/t11-,12-,15-,16-,17+,18+,20-/m0/s1

InChI Key

MPNQGWWVAITNMP-OVQIZMNKSA-N

Experimental Spectra

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

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Sinularia pavida	JEOL database	Shen, S., et al, Tetrahedron Lett. 53, 5759 (2012)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Sesquiterpenoid
Gamma butyrolactone
Oxolane
Carboxylic acid ester
Ketone
Lactone
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

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	2.04	ALOGPS
logP	3.29	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	17.31	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	60.44 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	89.77 m³·mol⁻¹	ChemAxon
Polarizability	36.32 Å³	ChemAxon
Number of Rings	4	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

Not Available

Chemspider ID

29215143

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71480867

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhang P, Li Y, Yan Z, Gong J, Yang Z: Asymmetric Total Synthesis of (-)-Pavidolide B via a Thiyl-Radical-Mediated [3 + 2] Annulation Reaction. J Org Chem. 2019 Dec 20;84(24):15958-15971. doi: 10.1021/acs.joc.9b02230. Epub 2019 Dec 5. [PubMed:31749362 ]
Rao P, Hu J, Xuan J, Ding H: Total Synthesis of (-)-Pavidolide B: A Ring Contraction Strategy. J Org Chem. 2019 Jul 19;84(14):9385-9392. doi: 10.1021/acs.joc.9b01308. Epub 2019 Jun 28. [PubMed:31251629 ]
He C, Xuan J, Rao P, Xie PP, Hong X, Lin X, Ding H: Total Syntheses of (+)-Sarcophytin, (+)-Chatancin, (-)-3-Oxochatancin, and (-)-Pavidolide B: A Divergent Approach. Angew Chem Int Ed Engl. 2019 Apr 1;58(15):5100-5104. doi: 10.1002/anie.201900782. Epub 2019 Mar 12. [PubMed:30908860 ]
Zhang PP, Yan ZM, Li YH, Gong JX, Yang Z: Enantioselective Total Synthesis of (-)-Pavidolide B. J Am Chem Soc. 2017 Oct 11;139(40):13989-13992. doi: 10.1021/jacs.7b07388. Epub 2017 Sep 7. [PubMed:28870073 ]
Shen, S., et al. (2012). Shen, S., et al, Tetrahedron Lett. 53, 5759 (2012). Tetrahedron Lett.

Showing NP-Card for pavidolide B (NP0041812)

MOL for NP0041812 (pavidolide B)

3D MOL for NP0041812 (pavidolide B)

3D SDF for NP0041812 (pavidolide B)

3D-SDF for NP0041812 (pavidolide B)

PDB for NP0041812 (pavidolide B)

3D PDB for NP0041812 (pavidolide B)

SMILES for NP0041812 (pavidolide B)

INCHI for NP0041812 (pavidolide B)

Structure for NP0041812 (pavidolide B)

3D Structure for NP0041812 (pavidolide B)