NP-MRD: Showing NP-Card for nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose (NP0042564)

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Record Information

Version

2.0

Created at

2021-06-21 00:12:04 UTC

Updated at

2021-06-30 00:17:43 UTC

NP-MRD ID

NP0042564

Secondary Accession Numbers

None

Natural Product Identification

Common Name

nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose

Provided By

JEOL Database JEOL Logo

Description

nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose is found in Aschersonia marginata BCC 28721. nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose was first documented in 2013 (Kornsakulkarn, J., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306212102123D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306212102123D          

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M  END
> <DATABASE_ID>
NP0042564

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C2=C(C(O[H])=C1[H])C(=O)C1=C(O[H])C3=C(O[C@]4(O[C@@]3([H])[C@]([H])(O[C@@]3([H])O[C@@]([H])(C([H])([H])O[H])[C@]([H])(OC([H])([H])[H])[C@@]([H])(O[H])[C@]3([H])O[H])C([H])([H])C4([H])[H])C([H])([H])[H])C([H])=C1C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H28O13/c1-27-4-3-13(37-26-23(35)22(34)25(36-2)15(8-28)38-26)24(40-27)18-14(39-27)7-11-17(21(18)33)20(32)16-10(19(11)31)5-9(29)6-12(16)30/h5-7,13,15,22-26,28-30,33-35H,3-4,8H2,1-2H3/t13-,15+,22+,23+,24+,25+,26+,27+/m1/s1

> <INCHI_KEY>
UJFRXIHRUIYXDV-SNLMKFAWSA-N

> <FORMULA>
C27H28O13

> <MOLECULAR_WEIGHT>
560.508

> <EXACT_MASS>
560.152990962

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
55.935741012566865

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(17R,20R)-20-{[(2S,3S,4S,5R,6S)-3,4-dihydroxy-6-(hydroxymethyl)-5-methoxyoxan-2-yl]oxy}-3,7,9-trihydroxy-17-methyl-16,21-dioxapentacyclo[15.3.1.0^{2,15}.0^{4,13}.0^{6,11}]henicosa-2(15),3,6(11),7,9,13-hexaene-5,12-dione

> <ALOGPS_LOGP>
1.63

> <JCHEM_LOGP>
1.9073504196666669

> <ALOGPS_LOGS>
-2.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.8265206927315925

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.151369180180265

> <JCHEM_PKA_STRONGEST_BASIC>
-2.98129245910322

> <JCHEM_POLAR_SURFACE_AREA>
201.67

> <JCHEM_REFRACTIVITY>
133.36299999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.43e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(17R,20R)-20-{[(2S,3S,4S,5R,6S)-3,4-dihydroxy-6-(hydroxymethyl)-5-methoxyoxan-2-yl]oxy}-3,7,9-trihydroxy-17-methyl-16,21-dioxapentacyclo[15.3.1.0^{2,15}.0^{4,13}.0^{6,11}]henicosa-2(15),3,6(11),7,9,13-hexaene-5,12-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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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       1.401  -6.438  -1.037  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.119  -5.418  -1.989  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.724  -4.178  -1.377  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.768  -3.083  -1.662  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.966  -3.165  -0.710  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.894  -2.116  -0.997  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.247  -1.736  -1.652  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.066  -1.546  -0.868  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.347  -1.804   0.507  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.050  -0.742   1.163  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.390  -1.280   2.628  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.980  -0.311   3.827  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.405   0.407   3.599  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.442  -0.054   4.615  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.353   1.871   3.662  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.549   2.520   2.436  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.964   3.842   2.445  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.107   4.512   1.221  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.804   3.871   0.010  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.355   2.539   0.007  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.027   1.882  -1.126  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.255   1.859   1.206  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.222   0.492   1.458  0.00  0.00           C+0
HETATM   24  O   UNK     0      -0.825   0.006   2.312  0.00  0.00           O+0
HETATM   25  C   UNK     0      -0.942   4.614  -1.258  0.00  0.00           C+0
HETATM   26  O   UNK     0      -0.661   4.067  -2.324  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.417   6.010  -1.257  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.569   6.720  -2.457  0.00  0.00           C+0
HETATM   29  O   UNK     0      -1.295   6.182  -3.686  0.00  0.00           O+0
HETATM   30  C   UNK     0      -2.017   8.039  -2.453  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.314   8.651  -1.241  0.00  0.00           C+0
HETATM   32  O   UNK     0      -2.755   9.939  -1.185  0.00  0.00           O+0
HETATM   33  C   UNK     0      -2.169   7.964  -0.040  0.00  0.00           C+0
HETATM   34  C   UNK     0      -1.719   6.638  -0.049  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.565   5.916   1.229  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.814   6.478   2.289  0.00  0.00           O+0
HETATM   37  C   UNK     0      -1.099  -2.457  -1.328  0.00  0.00           C+0
HETATM   38  O   UNK     0      -1.966  -1.776  -2.254  0.00  0.00           O+0
HETATM   39  C   UNK     0      -0.587  -3.725  -2.013  0.00  0.00           C+0
HETATM   40  O   UNK     0      -1.587  -4.753  -1.916  0.00  0.00           O+0
HETATM   41  H   UNK     0       1.718  -7.333  -1.577  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.501  -6.677  -0.462  0.00  0.00           H+0
HETATM   43  H   UNK     0       2.207  -6.129  -0.366  0.00  0.00           H+0
HETATM   44  H   UNK     0       0.570  -4.321  -0.299  0.00  0.00           H+0
HETATM   45  H   UNK     0       2.164  -3.219  -2.677  0.00  0.00           H+0
HETATM   46  H   UNK     0       2.662  -3.053   0.334  0.00  0.00           H+0
HETATM   47  H   UNK     0       3.493  -4.119  -0.812  0.00  0.00           H+0
HETATM   48  H   UNK     0       3.354  -1.360  -1.300  0.00  0.00           H+0
HETATM   49  H   UNK     0      -0.249  -0.510  -0.992  0.00  0.00           H+0
HETATM   50  H   UNK     0       1.974  -0.510   0.620  0.00  0.00           H+0
HETATM   51  H   UNK     0       2.466  -1.480   2.693  0.00  0.00           H+0
HETATM   52  H   UNK     0       0.885  -2.242   2.788  0.00  0.00           H+0
HETATM   53  H   UNK     0       0.970  -0.896   4.755  0.00  0.00           H+0
HETATM   54  H   UNK     0       1.767   0.443   3.964  0.00  0.00           H+0
HETATM   55  H   UNK     0      -1.580  -1.139   4.580  0.00  0.00           H+0
HETATM   56  H   UNK     0      -1.159   0.242   5.630  0.00  0.00           H+0
HETATM   57  H   UNK     0      -2.415   0.403   4.402  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.176   4.340   3.388  0.00  0.00           H+0
HETATM   59  H   UNK     0      -0.147   2.461  -1.903  0.00  0.00           H+0
HETATM   60  H   UNK     0       1.100   0.942   1.971  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.990   5.256  -3.562  0.00  0.00           H+0
HETATM   62  H   UNK     0      -2.127   8.567  -3.396  0.00  0.00           H+0
HETATM   63  H   UNK     0      -2.814  10.296  -2.088  0.00  0.00           H+0
HETATM   64  H   UNK     0      -2.407   8.464   0.897  0.00  0.00           H+0
HETATM   65  H   UNK     0      -1.728  -2.709  -0.465  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.651  -2.429  -2.496  0.00  0.00           H+0
HETATM   67  H   UNK     0      -0.449  -3.556  -3.089  0.00  0.00           H+0
HETATM   68  H   UNK     0      -1.161  -5.555  -2.276  0.00  0.00           H+0
CONECT    1    2   41   42   43                                             
CONECT    2    3    1                                                       
CONECT    3    2   39    4   44                                             
CONECT    4    3    7    5   45                                             
CONECT    5    6    4   46   47                                             
CONECT    6    5   48                                                       
CONECT    7    4    8                                                       
CONECT    8   37    7    9   49                                             
CONECT    9   10    8                                                       
CONECT   10   23   11    9   50                                             
CONECT   11   12   10   51   52                                             
CONECT   12   13   11   53   54                                             
CONECT   13   24   15   12   14                                             
CONECT   14   13   55   56   57                                             
CONECT   15   16   13                                                       
CONECT   16   22   15   17                                                  
CONECT   17   16   18   58                                                  
CONECT   18   35   19   17                                                  
CONECT   19   25   18   20                                                  
CONECT   20   21   19   22                                                  
CONECT   21   20   59                                                       
CONECT   22   16   23   20                                                  
CONECT   23   22   24   10   60                                             
CONECT   24   23   13                                                       
CONECT   25   26   27   19                                                  
CONECT   26   25                                                            
CONECT   27   34   28   25                                                  
CONECT   28   30   27   29                                                  
CONECT   29   28   61                                                       
CONECT   30   31   28   62                                                  
CONECT   31   33   30   32                                                  
CONECT   32   31   63                                                       
CONECT   33   34   31   64                                                  
CONECT   34   27   33   35                                                  
CONECT   35   34   36   18                                                  
CONECT   36   35                                                            
CONECT   37   38    8   39   65                                             
CONECT   38   37   66                                                       
CONECT   39   40   37    3   67                                             
CONECT   40   39   68                                                       
CONECT   41    1                                                            
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    3                                                            
CONECT   45    4                                                            
CONECT   46    5                                                            
CONECT   47    5                                                            
CONECT   48    6                                                            
CONECT   49    8                                                            
CONECT   50   10                                                            
CONECT   51   11                                                            
CONECT   52   11                                                            
CONECT   53   12                                                            
CONECT   54   12                                                            
CONECT   55   14                                                            
CONECT   56   14                                                            
CONECT   57   14                                                            
CONECT   58   17                                                            
CONECT   59   21                                                            
CONECT   60   23                                                            
CONECT   61   29                                                            
CONECT   62   30                                                            
CONECT   63   32                                                            
CONECT   64   33                                                            
CONECT   65   37                                                            
CONECT   66   38                                                            
CONECT   67   39                                                            
CONECT   68   40                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  146    0
END

RDKit          3D

68 73  0  0  0  0  0  0  0  0999 V2000
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M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₂₈O₁₃

Average Mass

560.5080 Da

Monoisotopic Mass

560.15299 Da

IUPAC Name

(17R,20R)-20-{[(2S,3S,4S,5R,6S)-3,4-dihydroxy-6-(hydroxymethyl)-5-methoxyoxan-2-yl]oxy}-3,7,9-trihydroxy-17-methyl-16,21-dioxapentacyclo[15.3.1.0^{2,15}.0^{4,13}.0^{6,11}]henicosa-2(15),3,6(11),7,9,13-hexaene-5,12-dione

Traditional Name

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C2=C(C(O[H])=C1[H])C(=O)C1=C(O[H])C3=C(O[C@]4(O[C@@]3([H])[C@]([H])(O[C@@]3([H])O[C@@]([H])(C([H])([H])O[H])[C@]([H])(OC([H])([H])[H])[C@@]([H])(O[H])[C@]3([H])O[H])C([H])([H])C4([H])[H])C([H])([H])[H])C([H])=C1C2=O

InChI Identifier

InChI=1S/C27H28O13/c1-27-4-3-13(37-26-23(35)22(34)25(36-2)15(8-28)38-26)24(40-27)18-14(39-27)7-11-17(21(18)33)20(32)16-10(19(11)31)5-9(29)6-12(16)30/h5-7,13,15,22-26,28-30,33-35H,3-4,8H2,1-2H3/t13-,15+,22+,23+,24+,25+,26+,27+/m1/s1

InChI Key

UJFRXIHRUIYXDV-SNLMKFAWSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
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, 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, 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, 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
Aschersonia marginata BCC 28721	JEOL database	Kornsakulkarn, J., et al, Tetrahedron Lett. 54, 3813 (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	1.63	ALOGPS
logP	1.91	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	7.15	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	201.67 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	133.36 m³·mol⁻¹	ChemAxon
Polarizability	55.94 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

Kornsakulkarn, J., et al. (2013). Kornsakulkarn, J., et al, Tetrahedron Lett. 54, 3813 (2013). Tetrahedron Lett.

Showing NP-Card for nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose (NP0042564)

MOL for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

3D MOL for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

3D SDF for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

3D-SDF for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

PDB for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

3D PDB for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

SMILES for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

INCHI for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

Structure for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)

3D Structure for NP0042564 (nidurufin-2'-(4-O-methyl)-beta-D-glucopyranose)