NP-MRD: Showing NP-Card for thorectidaeolide B (NP0043589)

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Record Information

Version

2.0

Created at

2021-06-21 00:57:16 UTC

Updated at

2021-06-30 00:19:21 UTC

NP-MRD ID

NP0043589

Secondary Accession Numbers

None

Natural Product Identification

Common Name

thorectidaeolide B

Provided By

JEOL Database JEOL Logo

Description

thorectidaeolide B is found in Hyrtios communis. thorectidaeolide B was first documented in 2013 (Li, J., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306212102573D          

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M  END


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   -4.5287   -2.2040   -3.4261 H   0  0  0  0  0  0  0  0  0  0  0  0
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  3  4  1  0  0  0  0
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  2  1  1  0  0  0  0
  6  8  2  0  0  0  0
  6  7  1  0  0  0  0
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 11 12  1  0  0  0  0
  8  9  1  0  0  0  0
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  2  3  2  0  0  0  0
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 22 55  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0043589

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])OC(=O)C([H])=C1C([H])([H])C([H])([H])C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])C1=C(C([H])([H])[H])C([H])([H])C([H])([H])C(=O)C1(C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C25H36O4/c1-17(10-7-11-20-16-23(27)29-24(20)28)8-6-9-18(2)12-14-21-19(3)13-15-22(26)25(21,4)5/h9-10,16,24,28H,6-8,11-15H2,1-5H3/b17-10+,18-9+/t24-/m0/s1

> <INCHI_KEY>
GLWQTMBDXUQDKL-JOIHSBEPSA-N

> <FORMULA>
C25H36O4

> <MOLECULAR_WEIGHT>
400.559

> <EXACT_MASS>
400.261359639

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
46.14313983957192

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)deca-3,7-dien-1-yl]-5-hydroxy-2,5-dihydrofuran-2-one

> <ALOGPS_LOGP>
5.82

> <JCHEM_LOGP>
5.983451297666667

> <ALOGPS_LOGS>
-5.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.790168777198923

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.244709966756093

> <JCHEM_PKA_STRONGEST_BASIC>
-4.27173086790421

> <JCHEM_POLAR_SURFACE_AREA>
63.6

> <JCHEM_REFRACTIVITY>
119.36579999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.14e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)deca-3,7-dien-1-yl]-5-hydroxy-5H-furan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 65 66  0  0  0  0  0  0  0  0999 V2000
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 22 55  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       1.458   2.282  -1.612  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.294   1.340  -0.442  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.673   1.647   0.728  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.033   3.018   0.971  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.150   3.423   0.065  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.441   2.651   0.256  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.293   3.089   1.417  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.803   1.698  -0.627  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.097   0.922  -0.613  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.251  -0.049  -1.802  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.369  -1.293  -1.867  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.476  -2.022  -3.183  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.593  -1.705  -0.845  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.656  -2.879  -0.783  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.194  -3.966   0.155  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.172  -5.006   0.483  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.219  -6.307   0.208  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.008  -6.893   0.778  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.294  -8.070   0.689  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.727  -5.930   1.391  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.059  -4.687   1.238  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.294  -4.137   2.487  0.00  0.00           O+0
HETATM   23  C   UNK     0       0.641   0.661   1.924  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.787   0.411   2.438  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.511   1.197   3.077  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.240  -0.712   1.543  0.00  0.00           C+0
HETATM   27  O   UNK     0       0.891  -1.773   2.071  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.377  -0.708   0.564  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.923  -0.012  -0.699  0.00  0.00           C+0
HETATM   30  H   UNK     0       0.776   2.002  -2.420  0.00  0.00           H+0
HETATM   31  H   UNK     0       1.290   3.330  -1.354  0.00  0.00           H+0
HETATM   32  H   UNK     0       2.483   2.237  -1.998  0.00  0.00           H+0
HETATM   33  H   UNK     0       0.823   3.774   0.861  0.00  0.00           H+0
HETATM   34  H   UNK     0      -0.283   3.118   2.015  0.00  0.00           H+0
HETATM   35  H   UNK     0      -1.364   4.485   0.246  0.00  0.00           H+0
HETATM   36  H   UNK     0      -0.861   3.382  -0.990  0.00  0.00           H+0
HETATM   37  H   UNK     0      -2.726   3.049   2.351  0.00  0.00           H+0
HETATM   38  H   UNK     0      -3.628   4.121   1.266  0.00  0.00           H+0
HETATM   39  H   UNK     0      -4.183   2.468   1.552  0.00  0.00           H+0
HETATM   40  H   UNK     0      -2.121   1.465  -1.444  0.00  0.00           H+0
HETATM   41  H   UNK     0      -4.209   0.381   0.333  0.00  0.00           H+0
HETATM   42  H   UNK     0      -4.925   1.641  -0.673  0.00  0.00           H+0
HETATM   43  H   UNK     0      -4.103   0.524  -2.728  0.00  0.00           H+0
HETATM   44  H   UNK     0      -5.294  -0.392  -1.815  0.00  0.00           H+0
HETATM   45  H   UNK     0      -4.529  -2.204  -3.426  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.982  -2.996  -3.184  0.00  0.00           H+0
HETATM   47  H   UNK     0      -3.036  -1.419  -3.983  0.00  0.00           H+0
HETATM   48  H   UNK     0      -2.601  -1.135   0.081  0.00  0.00           H+0
HETATM   49  H   UNK     0      -1.450  -3.304  -1.770  0.00  0.00           H+0
HETATM   50  H   UNK     0      -0.694  -2.498  -0.418  0.00  0.00           H+0
HETATM   51  H   UNK     0      -2.547  -3.518   1.093  0.00  0.00           H+0
HETATM   52  H   UNK     0      -3.072  -4.436  -0.307  0.00  0.00           H+0
HETATM   53  H   UNK     0      -1.973  -6.875  -0.306  0.00  0.00           H+0
HETATM   54  H   UNK     0       0.714  -4.006   0.684  0.00  0.00           H+0
HETATM   55  H   UNK     0       0.267  -3.338   2.585  0.00  0.00           H+0
HETATM   56  H   UNK     0      -1.240   1.312   2.859  0.00  0.00           H+0
HETATM   57  H   UNK     0      -1.435   0.043   1.638  0.00  0.00           H+0
HETATM   58  H   UNK     0      -0.803  -0.341   3.236  0.00  0.00           H+0
HETATM   59  H   UNK     0       1.608   0.454   3.877  0.00  0.00           H+0
HETATM   60  H   UNK     0       1.088   2.103   3.524  0.00  0.00           H+0
HETATM   61  H   UNK     0       2.525   1.438   2.737  0.00  0.00           H+0
HETATM   62  H   UNK     0       3.237  -0.205   1.019  0.00  0.00           H+0
HETATM   63  H   UNK     0       2.671  -1.739   0.340  0.00  0.00           H+0
HETATM   64  H   UNK     0       1.194  -0.632  -1.236  0.00  0.00           H+0
HETATM   65  H   UNK     0       2.796   0.089  -1.354  0.00  0.00           H+0
CONECT    1    2   30   31   32                                             
CONECT    2    1   29    3                                                  
CONECT    3    4    2   23                                                  
CONECT    4    3    5   33   34                                             
CONECT    5    4    6   35   36                                             
CONECT    6    5    8    7                                                  
CONECT    7    6   37   38   39                                             
CONECT    8    6    9   40                                                  
CONECT    9    8   10   41   42                                             
CONECT   10    9   11   43   44                                             
CONECT   11   12   10   13                                                  
CONECT   12   11   45   46   47                                             
CONECT   13   14   11   48                                                  
CONECT   14   13   15   49   50                                             
CONECT   15   14   16   51   52                                             
CONECT   16   15   17   21                                                  
CONECT   17   16   18   53                                                  
CONECT   18   17   20   19                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   16   22   54                                             
CONECT   22   21   55                                                       
CONECT   23   24   26   25    3                                             
CONECT   24   23   56   57   58                                             
CONECT   25   23   59   60   61                                             
CONECT   26   28   23   27                                                  
CONECT   27   26                                                            
CONECT   28   26   29   62   63                                             
CONECT   29   28    2   64   65                                             
CONECT   30    1                                                            
CONECT   31    1                                                            
CONECT   32    1                                                            
CONECT   33    4                                                            
CONECT   34    4                                                            
CONECT   35    5                                                            
CONECT   36    5                                                            
CONECT   37    7                                                            
CONECT   38    7                                                            
CONECT   39    7                                                            
CONECT   40    8                                                            
CONECT   41    9                                                            
CONECT   42    9                                                            
CONECT   43   10                                                            
CONECT   44   10                                                            
CONECT   45   12                                                            
CONECT   46   12                                                            
CONECT   47   12                                                            
CONECT   48   13                                                            
CONECT   49   14                                                            
CONECT   50   14                                                            
CONECT   51   15                                                            
CONECT   52   15                                                            
CONECT   53   17                                                            
CONECT   54   21                                                            
CONECT   55   22                                                            
CONECT   56   24                                                            
CONECT   57   24                                                            
CONECT   58   24                                                            
CONECT   59   25                                                            
CONECT   60   25                                                            
CONECT   61   25                                                            
CONECT   62   28                                                            
CONECT   63   28                                                            
CONECT   64   29                                                            
CONECT   65   29                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  132    0
END

RDKit          3D

65 66  0  0  0  0  0  0  0  0999 V2000
    1.4584    2.2821   -1.6118 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.7963    0.0894   -1.3537 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  4  1  0
 13 14  1  0
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 22 55  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₆O₄

Average Mass

400.5590 Da

Monoisotopic Mass

400.26136 Da

IUPAC Name

(5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)deca-3,7-dien-1-yl]-5-hydroxy-2,5-dihydrofuran-2-one

Traditional Name

(5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)deca-3,7-dien-1-yl]-5-hydroxy-5H-furan-2-one

CAS Registry Number

Not Available

SMILES

[H]O[C@@]1([H])OC(=O)C([H])=C1C([H])([H])C([H])([H])C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])C1=C(C([H])([H])[H])C([H])([H])C([H])([H])C(=O)C1(C([H])([H])[H])C([H])([H])[H]

InChI Identifier

InChI=1S/C25H36O4/c1-17(10-7-11-20-16-23(27)29-24(20)28)8-6-9-18(2)12-14-21-19(3)13-15-22(26)25(21,4)5/h9-10,16,24,28H,6-8,11-15H2,1-5H3/b17-10+,18-9+/t24-/m0/s1

InChI Key

GLWQTMBDXUQDKL-JOIHSBEPSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
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, 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, 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
Hyrtios communis	JEOL database	Li, J., et al, J. Nat. Prod. 76, 1492 (2013)

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	5.82	ALOGPS
logP	5.98	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	7.24	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	119.37 m³·mol⁻¹	ChemAxon
Polarizability	46.14 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	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

Li, J., et al. (2013). Li, J., et al, J. Nat. Prod. 76, 1492 (2013). J. Nat. Prod..

Showing NP-Card for thorectidaeolide B (NP0043589)

MOL for NP0043589 (thorectidaeolide B)

3D MOL for NP0043589 (thorectidaeolide B)

3D SDF for NP0043589 (thorectidaeolide B)

3D-SDF for NP0043589 (thorectidaeolide B)

PDB for NP0043589 (thorectidaeolide B)

3D PDB for NP0043589 (thorectidaeolide B)

SMILES for NP0043589 (thorectidaeolide B)

INCHI for NP0043589 (thorectidaeolide B)

Structure for NP0043589 (thorectidaeolide B)

3D Structure for NP0043589 (thorectidaeolide B)