NP-MRD: Showing NP-Card for nympholide B (NP0030771)

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Record Information

Version

2.0

Created at

2021-06-19 22:02:34 UTC

Updated at

2021-06-29 23:58:57 UTC

NP-MRD ID

NP0030771

Secondary Accession Numbers

None

Natural Product Identification

Common Name

nympholide B

Provided By

JEOL Database JEOL Logo

Description

nympholide B is found in Nymphaea lotus. nympholide B was first documented in 2003 (Elegami, A. A. E., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202100023D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306202100023D          

 71 76  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0030771

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C([H])=C(C([H])=C1[H])[C@]1([H])C2=C3OC(=C(O[H])C(=O)C3=C(O[H])C([H])=C2O[H])C2=C([H])C(O[C@@]3([H])O[C@@]([H])(C([H])([H])OC(=O)C1([H])[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]3([H])O[H])=C(O[H])C(O[H])=C2[H]

> <INCHI_IDENTIFIER>
InChI=1S/C30H26O15/c31-12-3-1-10(2-4-12)13-7-19(35)42-9-18-23(37)25(39)27(41)30(44-18)43-17-6-11(5-16(34)22(17)36)28-26(40)24(38)21-15(33)8-14(32)20(13)29(21)45-28/h1-6,8,13,18,23,25,27,30-34,36-37,39-41H,7,9H2/t13-,18+,23+,25-,27+,30+/m1/s1

> <INCHI_KEY>
GZTPVMNTZSEVRQ-CQAUYUSMSA-N

> <FORMULA>
C30H26O15

> <MOLECULAR_WEIGHT>
626.523

> <EXACT_MASS>
626.127170137

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
59.62871728915327

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(8R,9S,10R,11R,12S,17R)-4,5,9,10,11,19,21,24-octahydroxy-17-(4-hydroxyphenyl)-7,14,25,27-tetraoxapentacyclo[16.6.2.1^{2,6}.1^{8,12}.0^{22,26}]octacosa-1(24),2(28),3,5,18(26),19,21-heptaene-15,23-dione

> <ALOGPS_LOGP>
2.09

> <JCHEM_LOGP>
1.4487118753333328

> <ALOGPS_LOGS>
-2.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.839639797244444

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.180390485308267

> <JCHEM_PKA_STRONGEST_BASIC>
-3.678966921473039

> <JCHEM_POLAR_SURFACE_AREA>
253.12999999999994

> <JCHEM_REFRACTIVITY>
150.02839999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.13e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(8R,9S,10R,11R,12S,17R)-4,5,9,10,11,19,21,24-octahydroxy-17-(4-hydroxyphenyl)-7,14,25,27-tetraoxapentacyclo[16.6.2.1^{2,6}.1^{8,12}.0^{22,26}]octacosa-1(24),2(28),3,5,18(26),19,21-heptaene-15,23-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 71 76  0  0  0  0  0  0  0  0999 V2000
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   -3.0534   -1.8858   -0.6311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9209   -3.0562   -1.3208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6848   -0.9302   -3.1829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1852   -2.0267   -4.5867 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.9221    1.0753   -5.4174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3971    1.7124   -3.2307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8241    3.3974   -3.1154 H   0  0  0  0  0  0  0  0  0  0  0  0
 16 17  1  0
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  9 51  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      -0.257  -4.109  -0.078  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.497  -3.213   0.719  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.230  -3.036   2.027  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.115  -1.777   1.974  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.220  -1.749   0.914  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.663  -0.505   0.423  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.652  -0.430  -0.558  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.213  -1.596  -1.056  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.170  -1.480  -2.020  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.810  -2.837  -0.580  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.821  -2.911   0.406  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.645  -1.377   3.354  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.484  -2.212   4.110  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.791  -3.456   3.637  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.016  -1.798   5.333  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.725  -0.527   5.815  0.00  0.00           C+0
HETATM   17  O   UNK     0       3.296  -0.177   7.009  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.892   0.323   5.088  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.590   1.680   5.548  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.054   2.126   6.596  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.709   2.519   4.701  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.484   3.812   5.130  0.00  0.00           O+0
HETATM   23  C   UNK     0       0.196   1.981   3.578  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.491   0.693   3.156  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.343  -0.103   3.881  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.734   2.673   2.642  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.670   3.619   3.087  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.545   4.211   2.186  0.00  0.00           C+0
HETATM   29  O   UNK     0      -3.446   5.134   2.636  0.00  0.00           O+0
HETATM   30  C   UNK     0      -2.521   3.862   0.843  0.00  0.00           C+0
HETATM   31  O   UNK     0      -3.422   4.472   0.006  0.00  0.00           O+0
HETATM   32  C   UNK     0      -1.625   2.906   0.366  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.733   2.322   1.268  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.704   2.653  -0.976  0.00  0.00           O+0
HETATM   35  C   UNK     0      -1.114   1.441  -1.488  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.747   0.286  -0.936  0.00  0.00           O+0
HETATM   37  C   UNK     0      -1.292  -0.956  -1.512  0.00  0.00           C+0
HETATM   38  C   UNK     0      -1.991  -2.111  -0.774  0.00  0.00           C+0
HETATM   39  O   UNK     0      -1.416  -2.224   0.547  0.00  0.00           O+0
HETATM   40  C   UNK     0      -1.602  -0.983  -3.012  0.00  0.00           C+0
HETATM   41  O   UNK     0      -1.133  -2.184  -3.622  0.00  0.00           O+0
HETATM   42  C   UNK     0      -0.920   0.210  -3.682  0.00  0.00           C+0
HETATM   43  O   UNK     0      -1.279   0.231  -5.074  0.00  0.00           O+0
HETATM   44  C   UNK     0      -1.340   1.513  -3.013  0.00  0.00           C+0
HETATM   45  O   UNK     0      -0.599   2.589  -3.614  0.00  0.00           O+0
HETATM   46  H   UNK     0      -0.521  -2.960   2.823  0.00  0.00           H+0
HETATM   47  H   UNK     0       0.794  -3.952   2.228  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.427  -0.989   1.641  0.00  0.00           H+0
HETATM   49  H   UNK     0       2.240   0.420   0.807  0.00  0.00           H+0
HETATM   50  H   UNK     0       3.985   0.535  -0.930  0.00  0.00           H+0
HETATM   51  H   UNK     0       5.454  -2.373  -2.279  0.00  0.00           H+0
HETATM   52  H   UNK     0       4.246  -3.756  -0.959  0.00  0.00           H+0
HETATM   53  H   UNK     0       2.530  -3.896   0.766  0.00  0.00           H+0
HETATM   54  H   UNK     0       3.459  -3.863   4.216  0.00  0.00           H+0
HETATM   55  H   UNK     0       3.664  -2.446   5.916  0.00  0.00           H+0
HETATM   56  H   UNK     0       3.026   0.744   7.227  0.00  0.00           H+0
HETATM   57  H   UNK     0       0.984   3.903   5.968  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.742   3.901   4.133  0.00  0.00           H+0
HETATM   59  H   UNK     0      -3.946   5.401   1.839  0.00  0.00           H+0
HETATM   60  H   UNK     0      -3.294   4.041  -0.861  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.021   1.581   0.921  0.00  0.00           H+0
HETATM   62  H   UNK     0      -0.037   1.439  -1.276  0.00  0.00           H+0
HETATM   63  H   UNK     0      -0.210  -1.040  -1.342  0.00  0.00           H+0
HETATM   64  H   UNK     0      -3.053  -1.886  -0.631  0.00  0.00           H+0
HETATM   65  H   UNK     0      -1.921  -3.056  -1.321  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.685  -0.930  -3.183  0.00  0.00           H+0
HETATM   67  H   UNK     0      -1.185  -2.027  -4.587  0.00  0.00           H+0
HETATM   68  H   UNK     0       0.171   0.092  -3.658  0.00  0.00           H+0
HETATM   69  H   UNK     0      -0.922   1.075  -5.417  0.00  0.00           H+0
HETATM   70  H   UNK     0      -2.397   1.712  -3.231  0.00  0.00           H+0
HETATM   71  H   UNK     0      -0.824   3.397  -3.115  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    3   39    1                                                  
CONECT    3    2    4   46   47                                             
CONECT    4    5   12   48    3                                             
CONECT    5    6   11    4                                                  
CONECT    6    5    7   49                                                  
CONECT    7    6    8   50                                                  
CONECT    8    7   10    9                                                  
CONECT    9    8   51                                                       
CONECT   10    8   11   52                                                  
CONECT   11   10    5   53                                                  
CONECT   12   25   13    4                                                  
CONECT   13   15   12   14                                                  
CONECT   14   13   54                                                       
CONECT   15   13   16   55                                                  
CONECT   16   17   15   18                                                  
CONECT   17   16   56                                                       
CONECT   18   16   25   19                                                  
CONECT   19   20   18   21                                                  
CONECT   20   19                                                            
CONECT   21   22   19   23                                                  
CONECT   22   21   57                                                       
CONECT   23   26   21   24                                                  
CONECT   24   25   23                                                       
CONECT   25   12   18   24                                                  
CONECT   26   23   27   33                                                  
CONECT   27   26   28   58                                                  
CONECT   28   27   30   29                                                  
CONECT   29   28   59                                                       
CONECT   30   28   32   31                                                  
CONECT   31   30   60                                                       
CONECT   32   30   33   34                                                  
CONECT   33   32   26   61                                                  
CONECT   34   32   35                                                       
CONECT   35   36   44   34   62                                             
CONECT   36   37   35                                                       
CONECT   37   40   36   38   63                                             
CONECT   38   39   37   64   65                                             
CONECT   39    2   38                                                       
CONECT   40   37   42   41   66                                             
CONECT   41   40   67                                                       
CONECT   42   44   40   43   68                                             
CONECT   43   42   69                                                       
CONECT   44   45   35   42   70                                             
CONECT   45   44   71                                                       
CONECT   46    3                                                            
CONECT   47    3                                                            
CONECT   48    4                                                            
CONECT   49    6                                                            
CONECT   50    7                                                            
CONECT   51    9                                                            
CONECT   52   10                                                            
CONECT   53   11                                                            
CONECT   54   14                                                            
CONECT   55   15                                                            
CONECT   56   17                                                            
CONECT   57   22                                                            
CONECT   58   27                                                            
CONECT   59   29                                                            
CONECT   60   31                                                            
CONECT   61   33                                                            
CONECT   62   35                                                            
CONECT   63   37                                                            
CONECT   64   38                                                            
CONECT   65   38                                                            
CONECT   66   40                                                            
CONECT   67   41                                                            
CONECT   68   42                                                            
CONECT   69   43                                                            
CONECT   70   44                                                            
CONECT   71   45                                                            
MASTER        0    0    0    0    0    0    0    0   71    0  152    0
END

RDKit          3D

71 76  0  0  0  0  0  0  0  0999 V2000
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 19 20  2  0
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  2 39  1  0
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  2  1  2  0
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  6  7  1  0
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  4  5  1  0
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  7 50  1  0
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 11 53  1  0
  9 51  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₆O₁₅

Average Mass

626.5230 Da

Monoisotopic Mass

626.12717 Da

IUPAC Name

(8R,9S,10R,11R,12S,17R)-4,5,9,10,11,19,21,24-octahydroxy-17-(4-hydroxyphenyl)-7,14,25,27-tetraoxapentacyclo[16.6.2.1^{2,6}.1^{8,12}.0^{22,26}]octacosa-1(24),2(28),3,5,18(26),19,21-heptaene-15,23-dione

Traditional Name

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C([H])=C(C([H])=C1[H])[C@]1([H])C2=C3OC(=C(O[H])C(=O)C3=C(O[H])C([H])=C2O[H])C2=C([H])C(O[C@@]3([H])O[C@@]([H])(C([H])([H])OC(=O)C1([H])[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]3([H])O[H])=C(O[H])C(O[H])=C2[H]

InChI Identifier

InChI=1S/C30H26O15/c31-12-3-1-10(2-4-12)13-7-19(35)42-9-18-23(37)25(39)27(41)30(44-18)43-17-6-11(5-16(34)22(17)36)28-26(40)24(38)21-15(33)8-14(32)20(13)29(21)45-28/h1-6,8,13,18,23,25,27,30-34,36-37,39-41H,7,9H2/t13-,18+,23+,25-,27+,30+/m1/s1

InChI Key

GZTPVMNTZSEVRQ-CQAUYUSMSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
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, 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, 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, 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
Nymphaea lotus	JEOL database	Elegami, A. A. E., et al., Phytochemistry 63, 727 (2003)

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	2.09	ALOGPS
logP	1.45	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	6.18	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	253.13 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	150.03 m³·mol⁻¹	ChemAxon
Polarizability	59.63 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Elegami, A. A. E., et al. (2003). Elegami, A. A. E., et al., Phytochemistry 63, 727 (2003) . Phytochem..

Showing NP-Card for nympholide B (NP0030771)

MOL for NP0030771 (nympholide B)

3D MOL for NP0030771 (nympholide B)

3D SDF for NP0030771 (nympholide B)

3D-SDF for NP0030771 (nympholide B)

PDB for NP0030771 (nympholide B)

3D PDB for NP0030771 (nympholide B)

SMILES for NP0030771 (nympholide B)

INCHI for NP0030771 (nympholide B)

Structure for NP0030771 (nympholide B)

3D Structure for NP0030771 (nympholide B)