NP-MRD: Showing NP-Card for Cucumerin A (NP0026576)

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Record Information

Version

1.0

Created at

2021-06-19 18:25:33 UTC

Updated at

2021-06-29 23:52:12 UTC

NP-MRD ID

NP0026576

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cucumerin A

Provided By

JEOL Database JEOL Logo

Description

Cucumerin A is found in Averrhoa bilimbi , Cucumis sativus and Cucumis sativus. It was first documented in 2003 (McNally, D. J., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192120253D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306192120253D          

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M  END
> <DATABASE_ID>
NP0026576

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C([H])=C(C([H])=C1[H])C1=C([H])C(=O)C2=C(O[H])C(=C(O[H])C(=C2O1)[C@@]1([H])O[C@@]([H])(C([H])([H])O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H])[C@]([H])(C1=C([H])C([H])=C(O[H])C([H])=C1[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C29H28O11/c1-12(13-2-6-15(31)7-3-13)20-24(35)21-17(33)10-18(14-4-8-16(32)9-5-14)39-28(21)22(25(20)36)29-27(38)26(37)23(34)19(11-30)40-29/h2-10,12,19,23,26-27,29-32,34-38H,11H2,1H3/t12-,19-,23-,26+,27-,29+/m0/s1

> <INCHI_KEY>
VAVVYQGVFZBLHB-GNIJMHAISA-N

> <FORMULA>
C29H28O11

> <MOLECULAR_WEIGHT>
552.532

> <EXACT_MASS>
552.163161722

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
56.46896855148715

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[(1S)-1-(4-hydroxyphenyl)ethyl]-8-[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-4H-chromen-4-one

> <ALOGPS_LOGP>
2.01

> <JCHEM_LOGP>
2.024616030333333

> <ALOGPS_LOGS>
-3.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
7.19905442655436

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.827511164659811

> <JCHEM_PKA_STRONGEST_BASIC>
-2.979192630160272

> <JCHEM_POLAR_SURFACE_AREA>
197.36999999999998

> <JCHEM_REFRACTIVITY>
142.29890000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.67e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[(1S)-1-(4-hydroxyphenyl)ethyl]-8-[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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  4  5  1  0
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  6  7  1  0
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 12 50  1  0
 32 64  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      -0.582  -4.101   3.406  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.795  -4.222   2.732  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.066  -5.542   2.008  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.401  -5.922   1.772  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.702  -7.116   1.115  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.673  -7.943   0.688  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.007  -9.103   0.054  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.345  -7.593   0.904  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.045  -6.395   1.560  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.101  -2.997   1.866  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.358  -2.695   0.706  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.673  -3.531   0.364  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.640  -1.578  -0.110  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.215  -1.215  -1.320  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.631  -2.440  -1.967  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.385  -2.206  -3.165  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.689  -3.570  -3.803  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.492  -3.421  -4.970  0.00  0.00           O+0
HETATM   19  C   UNK     0      -2.676  -1.429  -2.854  0.00  0.00           C+0
HETATM   20  O   UNK     0      -3.413  -1.082  -4.033  0.00  0.00           O+0
HETATM   21  C   UNK     0      -2.329  -0.127  -2.132  0.00  0.00           C+0
HETATM   22  O   UNK     0      -3.531   0.540  -1.715  0.00  0.00           O+0
HETATM   23  C   UNK     0      -1.444  -0.375  -0.908  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.070   0.901  -0.370  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.710  -0.747   0.262  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.976   0.340  -0.539  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.994   1.208  -0.191  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.132   2.361  -1.100  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.984   3.023  -1.563  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.090   4.109  -2.435  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.344   4.536  -2.853  0.00  0.00           C+0
HETATM   32  O   UNK     0       3.401   5.598  -3.704  0.00  0.00           O+0
HETATM   33  C   UNK     0       4.496   3.892  -2.416  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.389   2.805  -1.543  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.781   1.052   0.881  0.00  0.00           C+0
HETATM   36  C   UNK     0       3.565  -0.112   1.748  0.00  0.00           C+0
HETATM   37  O   UNK     0       4.277  -0.314   2.727  0.00  0.00           O+0
HETATM   38  C   UNK     0       2.463  -1.023   1.403  0.00  0.00           C+0
HETATM   39  C   UNK     0       2.163  -2.139   2.199  0.00  0.00           C+0
HETATM   40  O   UNK     0       2.899  -2.426   3.323  0.00  0.00           O+0
HETATM   41  H   UNK     0      -0.753  -4.939   4.091  0.00  0.00           H+0
HETATM   42  H   UNK     0      -0.643  -3.176   3.992  0.00  0.00           H+0
HETATM   43  H   UNK     0      -1.412  -4.086   2.693  0.00  0.00           H+0
HETATM   44  H   UNK     0       1.489  -4.238   3.583  0.00  0.00           H+0
HETATM   45  H   UNK     0       3.216  -5.282   2.106  0.00  0.00           H+0
HETATM   46  H   UNK     0       3.736  -7.398   0.941  0.00  0.00           H+0
HETATM   47  H   UNK     0       1.192  -9.596  -0.131  0.00  0.00           H+0
HETATM   48  H   UNK     0      -0.467  -8.230   0.570  0.00  0.00           H+0
HETATM   49  H   UNK     0      -1.000  -6.131   1.706  0.00  0.00           H+0
HETATM   50  H   UNK     0      -0.756  -3.482  -0.610  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.401  -0.664  -2.042  0.00  0.00           H+0
HETATM   52  H   UNK     0      -0.777  -1.632  -3.878  0.00  0.00           H+0
HETATM   53  H   UNK     0      -2.215  -4.219  -3.094  0.00  0.00           H+0
HETATM   54  H   UNK     0      -0.753  -4.072  -4.074  0.00  0.00           H+0
HETATM   55  H   UNK     0      -2.543  -4.302  -5.388  0.00  0.00           H+0
HETATM   56  H   UNK     0      -3.342  -2.027  -2.220  0.00  0.00           H+0
HETATM   57  H   UNK     0      -3.376  -1.865  -4.627  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.832   0.569  -2.820  0.00  0.00           H+0
HETATM   59  H   UNK     0      -4.113   0.522  -2.503  0.00  0.00           H+0
HETATM   60  H   UNK     0      -2.027  -0.892  -0.136  0.00  0.00           H+0
HETATM   61  H   UNK     0      -1.913   1.391  -0.277  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.995   2.703  -1.240  0.00  0.00           H+0
HETATM   63  H   UNK     0       1.196   4.619  -2.783  0.00  0.00           H+0
HETATM   64  H   UNK     0       4.333   5.790  -3.901  0.00  0.00           H+0
HETATM   65  H   UNK     0       5.479   4.215  -2.744  0.00  0.00           H+0
HETATM   66  H   UNK     0       5.298   2.301  -1.224  0.00  0.00           H+0
HETATM   67  H   UNK     0       4.564   1.741   1.166  0.00  0.00           H+0
HETATM   68  H   UNK     0       3.598  -1.741   3.429  0.00  0.00           H+0
CONECT    1    2   41   42   43                                             
CONECT    2   10    1    3   44                                             
CONECT    3    2    4    9                                                  
CONECT    4    3    5   45                                                  
CONECT    5    4    6   46                                                  
CONECT    6    5    8    7                                                  
CONECT    7    6   47                                                       
CONECT    8    6    9   48                                                  
CONECT    9    8    3   49                                                  
CONECT   10   11    2   39                                                  
CONECT   11   10   13   12                                                  
CONECT   12   11   50                                                       
CONECT   13   14   11   25                                                  
CONECT   14   23   13   15   51                                             
CONECT   15   16   14                                                       
CONECT   16   19   15   17   52                                             
CONECT   17   18   16   53   54                                             
CONECT   18   17   55                                                       
CONECT   19   21   16   20   56                                             
CONECT   20   19   57                                                       
CONECT   21   23   19   22   58                                             
CONECT   22   21   59                                                       
CONECT   23   14   21   24   60                                             
CONECT   24   23   61                                                       
CONECT   25   26   13   38                                                  
CONECT   26   25   27                                                       
CONECT   27   35   26   28                                                  
CONECT   28   27   29   34                                                  
CONECT   29   28   30   62                                                  
CONECT   30   29   31   63                                                  
CONECT   31   30   33   32                                                  
CONECT   32   31   64                                                       
CONECT   33   31   34   65                                                  
CONECT   34   33   28   66                                                  
CONECT   35   36   27   67                                                  
CONECT   36   38   35   37                                                  
CONECT   37   36                                                            
CONECT   38   36   39   25                                                  
CONECT   39   40   10   38                                                  
CONECT   40   39   68                                                       
CONECT   41    1                                                            
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    2                                                            
CONECT   45    4                                                            
CONECT   46    5                                                            
CONECT   47    7                                                            
CONECT   48    8                                                            
CONECT   49    9                                                            
CONECT   50   12                                                            
CONECT   51   14                                                            
CONECT   52   16                                                            
CONECT   53   17                                                            
CONECT   54   17                                                            
CONECT   55   18                                                            
CONECT   56   19                                                            
CONECT   57   20                                                            
CONECT   58   21                                                            
CONECT   59   22                                                            
CONECT   60   23                                                            
CONECT   61   24                                                            
CONECT   62   29                                                            
CONECT   63   30                                                            
CONECT   64   32                                                            
CONECT   65   33                                                            
CONECT   66   34                                                            
CONECT   67   35                                                            
CONECT   68   40                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  144    0
END

RDKit          3D

68 72  0  0  0  0  0  0  0  0999 V2000
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M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₂₈O₁₁

Average Mass

552.5320 Da

Monoisotopic Mass

552.16316 Da

IUPAC Name

5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[(1S)-1-(4-hydroxyphenyl)ethyl]-8-[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-4H-chromen-4-one

Traditional Name

5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[(1S)-1-(4-hydroxyphenyl)ethyl]-8-[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C([H])=C(C([H])=C1[H])C1=C([H])C(=O)C2=C(O[H])C(=C(O[H])C(=C2O1)[C@@]1([H])O[C@@]([H])(C([H])([H])O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H])[C@]([H])(C1=C([H])C([H])=C(O[H])C([H])=C1[H])C([H])([H])[H]

InChI Identifier

InChI=1S/C29H28O11/c1-12(13-2-6-15(31)7-3-13)20-24(35)21-17(33)10-18(14-4-8-16(32)9-5-14)39-28(21)22(25(20)36)29-27(38)26(37)23(34)19(11-30)40-29/h2-10,12,19,23,26-27,29-32,34-38H,11H2,1H3/t12-,19-,23-,26+,27-,29+/m0/s1

InChI Key

VAVVYQGVFZBLHB-GNIJMHAISA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, DMSO-d6, 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
Averrhoa bilimbi	Plant	KNApSAcK
Cucumis sativus	LOTUS Database	35616633
Cucumis sativus L.	JEOL database	McNally, D. J., et al, J. Nat. Prod. 66, 1280 (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	2.01	ALOGPS
logP	2.02	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	5.83	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	197.37 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	142.3 m³·mol⁻¹	ChemAxon
Polarizability	56.47 Å³	ChemAxon
Number of Rings	5	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

McNally, D. J., et al. (2003). McNally, D. J., et al, J. Nat. Prod. 66, 1280 (2003). J. Nat. Prod..

Showing NP-Card for Cucumerin A (NP0026576)

MOL for NP0026576 (Cucumerin A)

3D MOL for NP0026576 (Cucumerin A)

3D SDF for NP0026576 (Cucumerin A)

3D-SDF for NP0026576 (Cucumerin A)

PDB for NP0026576 (Cucumerin A)

3D PDB for NP0026576 (Cucumerin A)

SMILES for NP0026576 (Cucumerin A)

INCHI for NP0026576 (Cucumerin A)

Structure for NP0026576 (Cucumerin A)

3D Structure for NP0026576 (Cucumerin A)