NP-MRD: Showing NP-Card for 1,10-seco-withametelin B (NP0033085)

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Record Information

Version

2.0

Created at

2021-06-19 23:43:50 UTC

Updated at

2021-06-30 00:02:39 UTC

NP-MRD ID

NP0033085

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1,10-seco-withametelin B

Provided By

JEOL Database JEOL Logo

Description

1,10-seco-withametelin B is found in Datura metel. 1,10-seco-withametelin B was first documented in 2007 (Pan, Y., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202101433D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306202101433D          

 69 74  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0033085

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]C([H])=C1C(=O)O[C@]2([H])C([H])([H])[C@]1(OC([H])([H])[C@@]2([H])[C@@]1([H])C([H])([H])C([H])([H])[C@@]2([H])[C@]3([H])C([H])([H])[C@@]4([H])OC(=O)C([H])([H])C([H])=C([H])C4=C(C([H])([H])[H])[C@]3([H])C([H])([H])C([H])([H])[C@@]12C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C28H36O5/c1-15-17-10-11-27(3)21(19(17)12-23-18(15)6-5-7-25(29)32-23)8-9-22(27)20-14-31-28(4)13-24(20)33-26(30)16(28)2/h5-6,17,19-24H,2,7-14H2,1,3-4H3/t17-,19+,20-,21-,22+,23+,24+,27+,28+/m0/s1

> <INCHI_KEY>
CNWDLTNXJPRUTP-ARNWAFANSA-N

> <FORMULA>
C28H36O5

> <MOLECULAR_WEIGHT>
452.591

> <EXACT_MASS>
452.256274259

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
51.23806377056617

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,9R,11S,12S,15R,16R)-2,16-dimethyl-15-[(1R,4R,5R)-1-methyl-8-methylidene-7-oxo-2,6-dioxabicyclo[3.3.1]nonan-4-yl]-8-oxatetracyclo[9.7.0.0^{3,9}.0^{12,16}]octadeca-2,4-dien-7-one

> <ALOGPS_LOGP>
4.02

> <JCHEM_LOGP>
3.9923335436666667

> <ALOGPS_LOGS>
-5.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.199426508206978

> <JCHEM_POLAR_SURFACE_AREA>
61.830000000000005

> <JCHEM_REFRACTIVITY>
125.4387

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.45e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,9R,11S,12S,15R,16R)-2,16-dimethyl-15-[(1R,4R,5R)-1-methyl-8-methylidene-7-oxo-2,6-dioxabicyclo[3.3.1]nonan-4-yl]-8-oxatetracyclo[9.7.0.0^{3,9}.0^{12,16}]octadeca-2,4-dien-7-one

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 69 74  0  0  0  0  0  0  0  0999 V2000
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    0.2000    1.9470    0.0427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2040    1.9179   -0.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
 31 30  1  0
 32 16  1  0
  3  2  1  0
 10 11  1  0
 12  6  1  0
 10  8  1  0
 16 15  1  0
 15 14  1  0
 14 13  1  0
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 27 28  1  0
  2  8  1  0
 32 33  1  1
  6  7  1  0
  3  4  2  0
 27 29  1  0
  2  1  2  3
 19 18  1  0
  6 36  1  1
 18 17  1  0
  8  9  1  1
 29 17  1  0
 26 19  1  0
  7  8  1  0
 19 20  1  0
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 26 25  1  0
  5  3  1  0
 20 21  1  0
 29 30  1  0
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 17 16  1  0
 21 23  1  0
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 32 31  1  0
 21 22  2  0
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  7 37  1  0
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 11 42  1  0
 11 43  1  0
 12 44  1  6
 18 52  1  0
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 19 54  1  1
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 23 55  1  0
 23 56  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  C   UNK     0      -5.963   0.885  -4.710  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.500   0.262  -3.609  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.367  -1.222  -3.690  0.00  0.00           C+0
HETATM    4  O   UNK     0      -5.710  -1.859  -4.680  0.00  0.00           O+0
HETATM    5  O   UNK     0      -4.826  -1.855  -2.619  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.463  -1.196  -1.381  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.381  -0.015  -1.151  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.137   0.945  -2.308  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.943   2.228  -2.044  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.753   1.352  -2.312  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.808   0.295  -2.484  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.963  -0.790  -1.415  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.446  -0.386   0.009  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.628  -1.561   0.999  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.406  -1.605   1.898  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.698  -0.262   1.704  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.771  -0.341   2.179  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.350   1.030   2.550  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.726   0.887   3.212  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.506   0.438   4.564  0.00  0.00           O+0
HETATM   21  C   UNK     0       3.483   0.522   5.497  0.00  0.00           C+0
HETATM   22  O   UNK     0       3.292   0.109   6.639  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.787   1.198   5.106  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.546   0.583   3.968  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.051   0.003   2.864  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.641  -0.100   2.506  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.187  -0.971   1.570  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.058  -1.988   0.862  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.707  -1.061   1.183  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.492  -0.574  -0.260  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.033  -0.697  -0.699  0.00  0.00           C+0
HETATM   32  C   UNK     0      -0.953   0.073   0.204  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.832   1.597  -0.012  0.00  0.00           C+0
HETATM   34  H   UNK     0      -6.215   0.336  -5.615  0.00  0.00           H+0
HETATM   35  H   UNK     0      -6.087   1.961  -4.759  0.00  0.00           H+0
HETATM   36  H   UNK     0      -4.645  -1.941  -0.601  0.00  0.00           H+0
HETATM   37  H   UNK     0      -6.430  -0.341  -1.134  0.00  0.00           H+0
HETATM   38  H   UNK     0      -5.169   0.455  -0.185  0.00  0.00           H+0
HETATM   39  H   UNK     0      -5.697   3.014  -2.766  0.00  0.00           H+0
HETATM   40  H   UNK     0      -7.023   2.046  -2.073  0.00  0.00           H+0
HETATM   41  H   UNK     0      -5.694   2.646  -1.060  0.00  0.00           H+0
HETATM   42  H   UNK     0      -2.916  -0.130  -3.488  0.00  0.00           H+0
HETATM   43  H   UNK     0      -1.810   0.730  -2.493  0.00  0.00           H+0
HETATM   44  H   UNK     0      -2.383  -1.658  -1.755  0.00  0.00           H+0
HETATM   45  H   UNK     0      -3.075   0.436   0.378  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.731  -2.527   0.492  0.00  0.00           H+0
HETATM   47  H   UNK     0      -3.537  -1.409   1.594  0.00  0.00           H+0
HETATM   48  H   UNK     0      -1.683  -1.767   2.945  0.00  0.00           H+0
HETATM   49  H   UNK     0      -0.771  -2.447   1.603  0.00  0.00           H+0
HETATM   50  H   UNK     0      -1.231   0.467   2.332  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.766  -0.932   3.108  0.00  0.00           H+0
HETATM   52  H   UNK     0       1.462   1.660   1.664  0.00  0.00           H+0
HETATM   53  H   UNK     0       0.667   1.546   3.236  0.00  0.00           H+0
HETATM   54  H   UNK     0       3.158   1.896   3.225  0.00  0.00           H+0
HETATM   55  H   UNK     0       5.433   1.139   5.992  0.00  0.00           H+0
HETATM   56  H   UNK     0       4.613   2.266   4.936  0.00  0.00           H+0
HETATM   57  H   UNK     0       6.630   0.605   4.078  0.00  0.00           H+0
HETATM   58  H   UNK     0       5.774  -0.415   2.165  0.00  0.00           H+0
HETATM   59  H   UNK     0       4.365  -1.607  -0.117  0.00  0.00           H+0
HETATM   60  H   UNK     0       4.952  -2.257   1.429  0.00  0.00           H+0
HETATM   61  H   UNK     0       3.511  -2.925   0.709  0.00  0.00           H+0
HETATM   62  H   UNK     0       1.435  -2.125   1.216  0.00  0.00           H+0
HETATM   63  H   UNK     0       2.100  -1.173  -0.951  0.00  0.00           H+0
HETATM   64  H   UNK     0       1.839   0.459  -0.376  0.00  0.00           H+0
HETATM   65  H   UNK     0      -0.043  -0.350  -1.734  0.00  0.00           H+0
HETATM   66  H   UNK     0      -0.226  -1.763  -0.717  0.00  0.00           H+0
HETATM   67  H   UNK     0      -1.406   2.149   0.741  0.00  0.00           H+0
HETATM   68  H   UNK     0       0.200   1.947   0.043  0.00  0.00           H+0
HETATM   69  H   UNK     0      -1.204   1.918  -0.984  0.00  0.00           H+0
CONECT    1    2   34   35                                                  
CONECT    2    3    8    1                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    6    3                                                       
CONECT    6   12    7   36    5                                             
CONECT    7    6    8   37   38                                             
CONECT    8   10    2    9    7                                             
CONECT    9    8   39   40   41                                             
CONECT   10   11    8                                                       
CONECT   11   10   12   42   43                                             
CONECT   12    6   13   11   44                                             
CONECT   13   14   32   12   45                                             
CONECT   14   15   13   46   47                                             
CONECT   15   16   14   48   49                                             
CONECT   16   32   15   17   50                                             
CONECT   17   18   29   16   51                                             
CONECT   18   19   17   52   53                                             
CONECT   19   18   26   20   54                                             
CONECT   20   19   21                                                       
CONECT   21   20   23   22                                                  
CONECT   22   21                                                            
CONECT   23   21   24   55   56                                             
CONECT   24   25   23   57                                                  
CONECT   25   26   24   58                                                  
CONECT   26   27   19   25                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27   59   60   61                                             
CONECT   29   27   17   30   62                                             
CONECT   30   31   29   63   64                                             
CONECT   31   30   32   65   66                                             
CONECT   32   16   13   33   31                                             
CONECT   33   32   67   68   69                                             
CONECT   34    1                                                            
CONECT   35    1                                                            
CONECT   36    6                                                            
CONECT   37    7                                                            
CONECT   38    7                                                            
CONECT   39    9                                                            
CONECT   40    9                                                            
CONECT   41    9                                                            
CONECT   42   11                                                            
CONECT   43   11                                                            
CONECT   44   12                                                            
CONECT   45   13                                                            
CONECT   46   14                                                            
CONECT   47   14                                                            
CONECT   48   15                                                            
CONECT   49   15                                                            
CONECT   50   16                                                            
CONECT   51   17                                                            
CONECT   52   18                                                            
CONECT   53   18                                                            
CONECT   54   19                                                            
CONECT   55   23                                                            
CONECT   56   23                                                            
CONECT   57   24                                                            
CONECT   58   25                                                            
CONECT   59   28                                                            
CONECT   60   28                                                            
CONECT   61   28                                                            
CONECT   62   29                                                            
CONECT   63   30                                                            
CONECT   64   30                                                            
CONECT   65   31                                                            
CONECT   66   31                                                            
CONECT   67   33                                                            
CONECT   68   33                                                            
CONECT   69   33                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  148    0
END

RDKit          3D

69 74  0  0  0  0  0  0  0  0999 V2000
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 24 57  1  0
 23 55  1  0
 23 56  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₆O₅

Average Mass

452.5910 Da

Monoisotopic Mass

452.25627 Da

IUPAC Name

(1R,9R,11S,12S,15R,16R)-2,16-dimethyl-15-[(1R,4R,5R)-1-methyl-8-methylidene-7-oxo-2,6-dioxabicyclo[3.3.1]nonan-4-yl]-8-oxatetracyclo[9.7.0.0^{3,9}.0^{12,16}]octadeca-2,4-dien-7-one

Traditional Name

(1R,9R,11S,12S,15R,16R)-2,16-dimethyl-15-[(1R,4R,5R)-1-methyl-8-methylidene-7-oxo-2,6-dioxabicyclo[3.3.1]nonan-4-yl]-8-oxatetracyclo[9.7.0.0^{3,9}.0^{12,16}]octadeca-2,4-dien-7-one

CAS Registry Number

Not Available

SMILES

[H]C([H])=C1C(=O)O[C@]2([H])C([H])([H])[C@]1(OC([H])([H])[C@@]2([H])[C@@]1([H])C([H])([H])C([H])([H])[C@@]2([H])[C@]3([H])C([H])([H])[C@@]4([H])OC(=O)C([H])([H])C([H])=C([H])C4=C(C([H])([H])[H])[C@]3([H])C([H])([H])C([H])([H])[C@@]12C([H])([H])[H])C([H])([H])[H]

InChI Identifier

InChI=1S/C28H36O5/c1-15-17-10-11-27(3)21(19(17)12-23-18(15)6-5-7-25(29)32-23)8-9-22(27)20-14-31-28(4)13-24(20)33-26(30)16(28)2/h5-6,17,19-24H,2,7-14H2,1,3-4H3/t17-,19+,20-,21-,22+,23+,24+,27+,28+/m0/s1

InChI Key

CNWDLTNXJPRUTP-ARNWAFANSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
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, 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, 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, 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, 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

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Datura metel	JEOL database	Pan, Y., et al, J. Nat. Prod. 70, 1127 (2007)

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	4.02	ALOGPS
logP	3.99	ChemAxon
logS	-5.5	ALOGPS
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	61.83 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	125.44 m³·mol⁻¹	ChemAxon
Polarizability	51.24 Å³	ChemAxon
Number of Rings	6	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

Not Available

References

General References

Pan, Y., et al. (2007). Pan, Y., et al, J. Nat. Prod. 70, 1127 (2007). J. Nat. Prod..

Showing NP-Card for 1,10-seco-withametelin B (NP0033085)

MOL for NP0033085 (1,10-seco-withametelin B)

3D MOL for NP0033085 (1,10-seco-withametelin B)

3D SDF for NP0033085 (1,10-seco-withametelin B)

3D-SDF for NP0033085 (1,10-seco-withametelin B)

PDB for NP0033085 (1,10-seco-withametelin B)

3D PDB for NP0033085 (1,10-seco-withametelin B)

SMILES for NP0033085 (1,10-seco-withametelin B)

INCHI for NP0033085 (1,10-seco-withametelin B)

Structure for NP0033085 (1,10-seco-withametelin B)

3D Structure for NP0033085 (1,10-seco-withametelin B)