NP-MRD: Showing NP-Card for ophiodilactone B (NP0038774)

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Record Information

Version

2.0

Created at

2021-06-20 21:22:47 UTC

Updated at

2021-06-30 00:11:44 UTC

NP-MRD ID

NP0038774

Secondary Accession Numbers

None

Natural Product Identification

Common Name

ophiodilactone B

Provided By

JEOL Database JEOL Logo

Description

(1S,9R,10R,11S,14S)-11,14-dibenzyl-14-hydroxy-10-phenyl-12,15-dioxatetracyclo[7.5.2.0¹,¹¹.0³,⁸]Hexadeca-3,5,7-triene-13,16-dione belongs to the class of organic compounds known as benzoxepines. These are organic compounds containing a benzene ring fused to an oxepine ring (an unsaturated seven-membered heterocycle with one oxygen atom replacing a carbon atom). ophiodilactone B is found in Ophiocoma scolopendrina. ophiodilactone B was first documented in 2009 (Ueoka, R., et al.). Based on a literature review very few articles have been published on (1S,9R,10R,11S,14S)-11,14-dibenzyl-14-hydroxy-10-phenyl-12,15-dioxatetracyclo[7.5.2.0¹,¹¹.0³,⁸]Hexadeca-3,5,7-triene-13,16-dione.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202123223D          

 67 73  0  0  0  0            999 V2000
   -1.1724   -3.5902    0.5643 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0253   -1.6886   -2.7391 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3833   -1.8915   -4.0846 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 67 73  0  0  0  0  0  0  0  0999 V2000
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   -0.8863   -2.5059    0.0732 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652306202123223D          

 67 73  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0038774

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1(C(=O)O[C@@]2(C([H])([H])C3=C([H])C([H])=C([H])C([H])=C3[H])[C@@]([H])(C3=C([H])C([H])=C([H])C([H])=C3[H])[C@@]3([H])C(=O)O[C@@]12C([H])([H])C1=C3C([H])=C([H])C([H])=C1[H])C([H])([H])C1=C([H])C([H])=C([H])C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C34H28O5/c35-30-28-27-19-11-10-18-26(27)22-34(38-30)32(37,20-23-12-4-1-5-13-23)31(36)39-33(34,21-24-14-6-2-7-15-24)29(28)25-16-8-3-9-17-25/h1-19,28-29,37H,20-22H2/t28-,29-,32+,33-,34-/m0/s1

> <INCHI_KEY>
NIOPNRXIINFUMO-NUTQVKNDSA-N

> <FORMULA>
C34H28O5

> <MOLECULAR_WEIGHT>
516.593

> <EXACT_MASS>
516.193674002

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
54.64400822988648

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,9R,10R,11S,14S)-11,14-dibenzyl-14-hydroxy-10-phenyl-12,15-dioxatetracyclo[7.5.2.0^{1,11}.0^{3,8}]hexadeca-3(8),4,6-triene-13,16-dione

> <ALOGPS_LOGP>
5.34

> <JCHEM_LOGP>
6.408511701999999

> <ALOGPS_LOGS>
-6.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.116514754055052

> <JCHEM_PKA_STRONGEST_BASIC>
-4.49743644657632

> <JCHEM_POLAR_SURFACE_AREA>
72.83

> <JCHEM_REFRACTIVITY>
145.59559999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.14e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,9R,10R,11S,14S)-11,14-dibenzyl-14-hydroxy-10-phenyl-12,15-dioxatetracyclo[7.5.2.0^{1,11}.0^{3,8}]hexadeca-3(8),4,6-triene-13,16-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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 17 50  1  0
 18 51  1  0
 19 52  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      -1.172  -3.590   0.564  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.886  -2.506   0.073  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.838  -1.588  -0.211  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.498  -0.428  -1.024  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.242  -0.899  -2.472  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.025  -1.689  -2.739  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.383  -1.892  -4.085  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.521  -2.620  -4.426  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.318  -3.165  -3.428  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.973  -2.984  -2.090  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.826  -2.253  -1.730  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.517  -2.071  -0.254  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.763  -0.608   0.185  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.075  -0.504   1.679  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.156  -0.873   2.674  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.490  -0.775   4.027  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.744  -0.308   4.409  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.666   0.066   3.437  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.335  -0.033   2.084  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.340   0.366  -0.359  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.279   1.481  -1.273  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.453   2.252  -0.698  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.298   3.084   0.419  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.388   3.786   0.936  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.641   3.674   0.339  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.806   2.862  -0.781  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.718   2.157  -1.299  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.031   1.034   0.723  0.00  0.00           O+0
HETATM   29  C   UNK     0      -2.324   1.283   0.379  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.057   2.043   0.995  0.00  0.00           O+0
HETATM   31  C   UNK     0      -2.699   0.546  -0.901  0.00  0.00           C+0
HETATM   32  O   UNK     0      -2.732   1.518  -1.956  0.00  0.00           O+0
HETATM   33  C   UNK     0      -4.101  -0.075  -0.702  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.577  -0.985  -1.812  0.00  0.00           C+0
HETATM   35  C   UNK     0      -4.955  -0.464  -3.057  0.00  0.00           C+0
HETATM   36  C   UNK     0      -5.381  -1.313  -4.080  0.00  0.00           C+0
HETATM   37  C   UNK     0      -5.438  -2.689  -3.869  0.00  0.00           C+0
HETATM   38  C   UNK     0      -5.072  -3.217  -2.634  0.00  0.00           C+0
HETATM   39  C   UNK     0      -4.648  -2.370  -1.609  0.00  0.00           C+0
HETATM   40  H   UNK     0      -2.063  -1.550  -2.790  0.00  0.00           H+0
HETATM   41  H   UNK     0      -1.237  -0.034  -3.147  0.00  0.00           H+0
HETATM   42  H   UNK     0      -0.235  -1.482  -4.883  0.00  0.00           H+0
HETATM   43  H   UNK     0       1.781  -2.766  -5.472  0.00  0.00           H+0
HETATM   44  H   UNK     0       3.204  -3.737  -3.689  0.00  0.00           H+0
HETATM   45  H   UNK     0       2.611  -3.425  -1.325  0.00  0.00           H+0
HETATM   46  H   UNK     0       1.181  -2.726   0.328  0.00  0.00           H+0
HETATM   47  H   UNK     0       1.703  -0.346  -0.321  0.00  0.00           H+0
HETATM   48  H   UNK     0      -0.841  -1.226   2.426  0.00  0.00           H+0
HETATM   49  H   UNK     0      -0.236  -1.061   4.785  0.00  0.00           H+0
HETATM   50  H   UNK     0       1.999  -0.229   5.462  0.00  0.00           H+0
HETATM   51  H   UNK     0       3.644   0.439   3.730  0.00  0.00           H+0
HETATM   52  H   UNK     0       3.076   0.276   1.349  0.00  0.00           H+0
HETATM   53  H   UNK     0       0.601   1.041  -2.222  0.00  0.00           H+0
HETATM   54  H   UNK     0      -0.469   2.239  -1.529  0.00  0.00           H+0
HETATM   55  H   UNK     0       0.330   3.193   0.904  0.00  0.00           H+0
HETATM   56  H   UNK     0       2.256   4.421   1.809  0.00  0.00           H+0
HETATM   57  H   UNK     0       4.487   4.223   0.743  0.00  0.00           H+0
HETATM   58  H   UNK     0       4.781   2.779  -1.252  0.00  0.00           H+0
HETATM   59  H   UNK     0       2.869   1.530  -2.175  0.00  0.00           H+0
HETATM   60  H   UNK     0      -3.398   2.189  -1.707  0.00  0.00           H+0
HETATM   61  H   UNK     0      -4.846   0.729  -0.611  0.00  0.00           H+0
HETATM   62  H   UNK     0      -4.150  -0.611   0.256  0.00  0.00           H+0
HETATM   63  H   UNK     0      -4.921   0.606  -3.244  0.00  0.00           H+0
HETATM   64  H   UNK     0      -5.671  -0.900  -5.043  0.00  0.00           H+0
HETATM   65  H   UNK     0      -5.770  -3.349  -4.666  0.00  0.00           H+0
HETATM   66  H   UNK     0      -5.116  -4.290  -2.465  0.00  0.00           H+0
HETATM   67  H   UNK     0      -4.363  -2.807  -0.652  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    3    1   12                                                  
CONECT    3    2    4                                                       
CONECT    4   20    3    5   31                                             
CONECT    5    4    6   40   41                                             
CONECT    6    5   11    7                                                  
CONECT    7    8    6   42                                                  
CONECT    8    9    7   43                                                  
CONECT    9   10    8   44                                                  
CONECT   10   11    9   45                                                  
CONECT   11    6   10   12                                                  
CONECT   12   13    2   11   46                                             
CONECT   13   20   12   14   47                                             
CONECT   14   13   15   19                                                  
CONECT   15   14   16   48                                                  
CONECT   16   15   17   49                                                  
CONECT   17   16   18   50                                                  
CONECT   18   17   19   51                                                  
CONECT   19   18   14   52                                                  
CONECT   20   28   21    4   13                                             
CONECT   21   20   22   53   54                                             
CONECT   22   21   23   27                                                  
CONECT   23   22   24   55                                                  
CONECT   24   23   25   56                                                  
CONECT   25   24   26   57                                                  
CONECT   26   25   27   58                                                  
CONECT   27   26   22   59                                                  
CONECT   28   20   29                                                       
CONECT   29   30   31   28                                                  
CONECT   30   29                                                            
CONECT   31   32   33    4   29                                             
CONECT   32   31   60                                                       
CONECT   33   31   34   61   62                                             
CONECT   34   39   33   35                                                  
CONECT   35   34   36   63                                                  
CONECT   36   35   37   64                                                  
CONECT   37   36   38   65                                                  
CONECT   38   39   37   66                                                  
CONECT   39   38   34   67                                                  
CONECT   40    5                                                            
CONECT   41    5                                                            
CONECT   42    7                                                            
CONECT   43    8                                                            
CONECT   44    9                                                            
CONECT   45   10                                                            
CONECT   46   12                                                            
CONECT   47   13                                                            
CONECT   48   15                                                            
CONECT   49   16                                                            
CONECT   50   17                                                            
CONECT   51   18                                                            
CONECT   52   19                                                            
CONECT   53   21                                                            
CONECT   54   21                                                            
CONECT   55   23                                                            
CONECT   56   24                                                            
CONECT   57   25                                                            
CONECT   58   26                                                            
CONECT   59   27                                                            
CONECT   60   32                                                            
CONECT   61   33                                                            
CONECT   62   33                                                            
CONECT   63   35                                                            
CONECT   64   36                                                            
CONECT   65   37                                                            
CONECT   66   38                                                            
CONECT   67   39                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  146    0
END

RDKit          3D

67 73  0  0  0  0  0  0  0  0999 V2000
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 17 50  1  0
 18 51  1  0
 19 52  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₄H₂₈O₅

Average Mass

516.5930 Da

Monoisotopic Mass

516.19367 Da

IUPAC Name

(1S,9R,10R,11S,14S)-11,14-dibenzyl-14-hydroxy-10-phenyl-12,15-dioxatetracyclo[7.5.2.0^{1,11}.0^{3,8}]hexadeca-3(8),4,6-triene-13,16-dione

Traditional Name

(1S,9R,10R,11S,14S)-11,14-dibenzyl-14-hydroxy-10-phenyl-12,15-dioxatetracyclo[7.5.2.0^{1,11}.0^{3,8}]hexadeca-3(8),4,6-triene-13,16-dione

CAS Registry Number

Not Available

SMILES

[H]O[C@@]1(C(=O)O[C@@]2(C([H])([H])C3=C([H])C([H])=C([H])C([H])=C3[H])[C@@]([H])(C3=C([H])C([H])=C([H])C([H])=C3[H])[C@@]3([H])C(=O)O[C@@]12C([H])([H])C1=C3C([H])=C([H])C([H])=C1[H])C([H])([H])C1=C([H])C([H])=C([H])C([H])=C1[H]

InChI Identifier

InChI=1S/C34H28O5/c35-30-28-27-19-11-10-18-26(27)22-34(38-30)32(37,20-23-12-4-1-5-13-23)31(36)39-33(34,21-24-14-6-2-7-15-24)29(28)25-16-8-3-9-17-25/h1-19,28-29,37H,20-22H2/t28-,29-,32+,33-,34-/m0/s1

InChI Key

NIOPNRXIINFUMO-NUTQVKNDSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, CD₃OD, 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
Ophiocoma scolopendrina	JEOL database	Ueoka, R., et al, J. Org. Chem. 74, 4396 (2009)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzoxepines. These are organic compounds containing a benzene ring fused to an oxepine ring (an unsaturated seven-membered heterocycle with one oxygen atom replacing a carbon atom).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzoxepines

Sub Class

Not Available

Direct Parent

Benzoxepines

Alternative Parents

Substituents

Benzoxepine
Furopyran
Delta valerolactone
Delta_valerolactone
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Gamma butyrolactone
Monosaccharide
Oxane
Pyran
Benzenoid
Furan
Oxolane
Tertiary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Carboxylic acid derivative
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	5.34	ALOGPS
logP	6.41	ChemAxon
logS	-6.1	ALOGPS
pKa (Strongest Acidic)	11.12	ChemAxon
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.83 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	145.6 m³·mol⁻¹	ChemAxon
Polarizability	54.64 Å³	ChemAxon
Number of Rings	7	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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

27024994

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44133101

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ueoka, R., et al. (2009). Ueoka, R., et al, J. Org. Chem. 74, 4396 (2009). J. Org. Chem..

Showing NP-Card for ophiodilactone B (NP0038774)

MOL for NP0038774 (ophiodilactone B)

3D MOL for NP0038774 (ophiodilactone B)

3D SDF for NP0038774 (ophiodilactone B)

3D-SDF for NP0038774 (ophiodilactone B)

PDB for NP0038774 (ophiodilactone B)

3D PDB for NP0038774 (ophiodilactone B)

SMILES for NP0038774 (ophiodilactone B)

INCHI for NP0038774 (ophiodilactone B)

Structure for NP0038774 (ophiodilactone B)

3D Structure for NP0038774 (ophiodilactone B)