NP-MRD: Showing NP-Card for Vibsanin I (NP0025661)

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Record Information

Version

2.0

Created at

2021-06-19 17:43:49 UTC

Updated at

2021-06-29 23:50:45 UTC

NP-MRD ID

NP0025661

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Vibsanin I

Provided By

JEOL Database JEOL Logo

Description

Vibsanin I is found in Viburnum odoratissimum. Vibsanin I was first documented in 2001 (Kubo, M., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192119433D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306192119433D          

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M  END
> <DATABASE_ID>
NP0025661

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OO[C@@]([H])(C(=C([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])[C@@]1(C([H])([H])[H])C([H])([H])C([H])=C(C(=O)[C@@]([H])(C([H])([H])C(=O)C([H])([H])[H])[C@]1([H])C(\[H])=C(\[H])OC(=O)C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C25H36O7/c1-16(2)13-23(28)31-12-9-21-20(14-18(5)27)24(29)19(15-26)7-10-25(21,6)11-8-22(32-30)17(3)4/h7,9,12-13,20-22,26,30H,3,8,10-11,14-15H2,1-2,4-6H3/b12-9-/t20-,21-,22+,25+/m0/s1

> <INCHI_KEY>
UJJUMNMPDZRFHA-YRDPNEFQSA-N

> <FORMULA>
C25H36O7

> <MOLECULAR_WEIGHT>
448.556

> <EXACT_MASS>
448.246103499

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
48.53051853183155

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(Z)-2-[(1S,2S,7S)-2-[(3R)-3-hydroperoxy-4-methylpent-4-en-1-yl]-5-(hydroxymethyl)-2-methyl-6-oxo-7-(2-oxopropyl)cyclohept-4-en-1-yl]ethenyl 3-methylbut-2-enoate

> <ALOGPS_LOGP>
2.81

> <JCHEM_LOGP>
3.933179131666667

> <ALOGPS_LOGS>
-4.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.96688475241156

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.711121032665613

> <JCHEM_PKA_STRONGEST_BASIC>
-2.811943032757034

> <JCHEM_POLAR_SURFACE_AREA>
110.13

> <JCHEM_REFRACTIVITY>
124.01109999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(Z)-2-[(1S,2S,7S)-2-[(3R)-3-hydroperoxy-4-methylpent-4-en-1-yl]-5-(hydroxymethyl)-2-methyl-6-oxo-7-(2-oxopropyl)cyclohept-4-en-1-yl]ethenyl 3-methylbut-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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 19 56  1  0
 19 57  1  0
 23 60  1  0
  6 41  1  0
  6 42  1  0
  5 39  1  0
  5 40  1  0
  4 38  1  6
  3 35  1  0
  3 36  1  0
  3 37  1  0
  1 33  1  0
  1 34  1  0
 32 68  1  0
M  END

HEADER    PROTEIN                                 19-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-21         0                                  
HETATM    1  C   UNK     0       0.704  -3.182  -3.831  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.162  -2.394  -2.886  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.437  -1.060  -3.240  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.124  -2.818  -1.425  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.910  -1.851  -0.522  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.078  -2.410   0.902  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.651  -1.427   1.982  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.957  -2.297   3.237  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.029  -0.850   1.536  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.051   0.311   0.589  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.469   1.517   0.715  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.645   2.582  -0.337  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.384   2.911  -0.909  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.612   1.936   1.876  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.156   3.086   1.871  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.268   0.943   2.998  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.392   1.673   4.039  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.173   2.763   4.757  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.394   3.971   5.205  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.371   2.640   5.012  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.595  -0.299   2.331  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.602  -0.845   3.094  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.850  -0.936   2.616  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.190  -0.532   1.325  0.00  0.00           O+0
HETATM   25  C   UNK     0      -3.443  -0.881   0.896  0.00  0.00           C+0
HETATM   26  O   UNK     0      -4.311  -1.458   1.531  0.00  0.00           O+0
HETATM   27  C   UNK     0      -3.575  -0.386  -0.500  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.476  -0.804  -1.410  0.00  0.00           C+0
HETATM   29  C   UNK     0      -5.481  -1.904  -1.204  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.525  -0.167  -2.775  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.242  -2.835  -0.981  0.00  0.00           O+0
HETATM   32  O   UNK     0      -1.807  -4.106  -1.420  0.00  0.00           O+0
HETATM   33  H   UNK     0       1.133  -4.150  -3.588  0.00  0.00           H+0
HETATM   34  H   UNK     0       0.731  -2.884  -4.875  0.00  0.00           H+0
HETATM   35  H   UNK     0      -0.408  -0.872  -4.318  0.00  0.00           H+0
HETATM   36  H   UNK     0      -1.485  -1.016  -2.930  0.00  0.00           H+0
HETATM   37  H   UNK     0       0.108  -0.247  -2.752  0.00  0.00           H+0
HETATM   38  H   UNK     0       0.547  -3.825  -1.306  0.00  0.00           H+0
HETATM   39  H   UNK     0       1.899  -1.678  -0.960  0.00  0.00           H+0
HETATM   40  H   UNK     0       0.383  -0.893  -0.482  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.117  -2.805   1.253  0.00  0.00           H+0
HETATM   42  H   UNK     0       1.742  -3.284   0.832  0.00  0.00           H+0
HETATM   43  H   UNK     0       2.252  -1.679   4.091  0.00  0.00           H+0
HETATM   44  H   UNK     0       1.096  -2.904   3.538  0.00  0.00           H+0
HETATM   45  H   UNK     0       2.779  -2.996   3.038  0.00  0.00           H+0
HETATM   46  H   UNK     0       3.633  -0.566   2.409  0.00  0.00           H+0
HETATM   47  H   UNK     0       3.606  -1.663   1.071  0.00  0.00           H+0
HETATM   48  H   UNK     0       3.658   0.136  -0.301  0.00  0.00           H+0
HETATM   49  H   UNK     0       3.295   2.245  -1.152  0.00  0.00           H+0
HETATM   50  H   UNK     0       3.096   3.487   0.084  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.889   3.355  -0.191  0.00  0.00           H+0
HETATM   52  H   UNK     0       2.201   0.665   3.498  0.00  0.00           H+0
HETATM   53  H   UNK     0       0.052   0.993   4.827  0.00  0.00           H+0
HETATM   54  H   UNK     0      -0.491   2.117   3.564  0.00  0.00           H+0
HETATM   55  H   UNK     0      -0.377   3.665   5.916  0.00  0.00           H+0
HETATM   56  H   UNK     0       1.067   4.683   5.691  0.00  0.00           H+0
HETATM   57  H   UNK     0      -0.062   4.456   4.338  0.00  0.00           H+0
HETATM   58  H   UNK     0       0.196   0.061   1.375  0.00  0.00           H+0
HETATM   59  H   UNK     0      -0.430  -1.196   4.110  0.00  0.00           H+0
HETATM   60  H   UNK     0      -2.672  -1.337   3.198  0.00  0.00           H+0
HETATM   61  H   UNK     0      -2.864   0.394  -0.760  0.00  0.00           H+0
HETATM   62  H   UNK     0      -5.246  -2.555  -0.360  0.00  0.00           H+0
HETATM   63  H   UNK     0      -5.515  -2.552  -2.087  0.00  0.00           H+0
HETATM   64  H   UNK     0      -6.478  -1.479  -1.053  0.00  0.00           H+0
HETATM   65  H   UNK     0      -4.312  -0.911  -3.549  0.00  0.00           H+0
HETATM   66  H   UNK     0      -5.519   0.254  -2.959  0.00  0.00           H+0
HETATM   67  H   UNK     0      -3.797   0.643  -2.883  0.00  0.00           H+0
HETATM   68  H   UNK     0      -2.298  -3.748  -2.181  0.00  0.00           H+0
CONECT    1    2   33   34                                                  
CONECT    2    4    3    1                                                  
CONECT    3    2   35   36   37                                             
CONECT    4    5   31    2   38                                             
CONECT    5    6    4   39   40                                             
CONECT    6    7    5   41   42                                             
CONECT    7   21    6    9    8                                             
CONECT    8    7   43   44   45                                             
CONECT    9   10    7   46   47                                             
CONECT   10   11    9   48                                                  
CONECT   11   12   14   10                                                  
CONECT   12   11   13   49   50                                             
CONECT   13   12   51                                                       
CONECT   14   16   15   11                                                  
CONECT   15   14                                                            
CONECT   16   14   17   21   52                                             
CONECT   17   16   18   53   54                                             
CONECT   18   17   19   20                                                  
CONECT   19   18   55   56   57                                             
CONECT   20   18                                                            
CONECT   21   16    7   22   58                                             
CONECT   22   23   21   59                                                  
CONECT   23   22   24   60                                                  
CONECT   24   25   23                                                       
CONECT   25   27   24   26                                                  
CONECT   26   25                                                            
CONECT   27   28   25   61                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28   62   63   64                                             
CONECT   30   28   65   66   67                                             
CONECT   31    4   32                                                       
CONECT   32   31   68                                                       
CONECT   33    1                                                            
CONECT   34    1                                                            
CONECT   35    3                                                            
CONECT   36    3                                                            
CONECT   37    3                                                            
CONECT   38    4                                                            
CONECT   39    5                                                            
CONECT   40    5                                                            
CONECT   41    6                                                            
CONECT   42    6                                                            
CONECT   43    8                                                            
CONECT   44    8                                                            
CONECT   45    8                                                            
CONECT   46    9                                                            
CONECT   47    9                                                            
CONECT   48   10                                                            
CONECT   49   12                                                            
CONECT   50   12                                                            
CONECT   51   13                                                            
CONECT   52   16                                                            
CONECT   53   17                                                            
CONECT   54   17                                                            
CONECT   55   19                                                            
CONECT   56   19                                                            
CONECT   57   19                                                            
CONECT   58   21                                                            
CONECT   59   22                                                            
CONECT   60   23                                                            
CONECT   61   27                                                            
CONECT   62   29                                                            
CONECT   63   29                                                            
CONECT   64   29                                                            
CONECT   65   30                                                            
CONECT   66   30                                                            
CONECT   67   30                                                            
CONECT   68   32                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  136    0
END

RDKit          3D

68 68  0  0  0  0  0  0  0  0999 V2000
    0.7038   -3.1819   -3.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.4690    1.5171    0.7151 C   0  0  0  0  0  0  0  0  0  0  0  0
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  5 39  1  0
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  3 37  1  0
  1 33  1  0
  1 34  1  0
 32 68  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₆O₇

Average Mass

448.5560 Da

Monoisotopic Mass

448.24610 Da

IUPAC Name

(Z)-2-[(1S,2S,7S)-2-[(3R)-3-hydroperoxy-4-methylpent-4-en-1-yl]-5-(hydroxymethyl)-2-methyl-6-oxo-7-(2-oxopropyl)cyclohept-4-en-1-yl]ethenyl 3-methylbut-2-enoate

Traditional Name

(Z)-2-[(1S,2S,7S)-2-[(3R)-3-hydroperoxy-4-methylpent-4-en-1-yl]-5-(hydroxymethyl)-2-methyl-6-oxo-7-(2-oxopropyl)cyclohept-4-en-1-yl]ethenyl 3-methylbut-2-enoate

CAS Registry Number

Not Available

SMILES

[H]OO[C@@]([H])(C(=C([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])[C@@]1(C([H])([H])[H])C([H])([H])C([H])=C(C(=O)[C@@]([H])(C([H])([H])C(=O)C([H])([H])[H])[C@]1([H])C(\[H])=C(\[H])OC(=O)C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])O[H]

InChI Identifier

InChI=1S/C25H36O7/c1-16(2)13-23(28)31-12-9-21-20(14-18(5)27)24(29)19(15-26)7-10-25(21,6)11-8-22(32-30)17(3)4/h7,9,12-13,20-22,26,30H,3,8,10-11,14-15H2,1-2,4-6H3/b12-9-/t20-,21-,22+,25+/m0/s1

InChI Key

UJJUMNMPDZRFHA-YRDPNEFQSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, C₆D₆, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, C₆D₆, 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
Viburnum odoratissimum	JEOL database	Kubo, M., et al, Chem. Pharm. Bull. 49, 242 (2001)

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	2.81	ALOGPS
logP	3.93	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	11.71	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	110.13 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	124.01 m³·mol⁻¹	ChemAxon
Polarizability	48.53 Å³	ChemAxon
Number of Rings	1	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

Kubo, M., et al. (2001). Kubo, M., et al, Chem. Pharm. Bull. 49, 242 (2001). Chem. Pharm. Bull..

Showing NP-Card for Vibsanin I (NP0025661)

MOL for NP0025661 (Vibsanin I)

3D MOL for NP0025661 (Vibsanin I)

3D SDF for NP0025661 (Vibsanin I)

3D-SDF for NP0025661 (Vibsanin I)

PDB for NP0025661 (Vibsanin I)

3D PDB for NP0025661 (Vibsanin I)

SMILES for NP0025661 (Vibsanin I)

INCHI for NP0025661 (Vibsanin I)

Structure for NP0025661 (Vibsanin I)

3D Structure for NP0025661 (Vibsanin I)