NP-MRD: Showing NP-Card for (+)-Ardimerin (NP0076182)

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Record Information

Version

1.0

Created at

2022-04-28 21:20:22 UTC

Updated at

2022-04-28 21:20:23 UTC

NP-MRD ID

NP0076182

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Ardimerin

Description

Ardimerin belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. (+)-Ardimerin is found in Ardisia japonica . It was first documented in 2007 (PMID: 17397219). Based on a literature review very few articles have been published on ardimerin (PMID: 24712737).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282223202D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282223202D          

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   -0.6526    4.9219    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3671    3.6844    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3671    2.0344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0618    1.2094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6259    0.7969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3404    1.2094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3404    2.0344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6259    2.4469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6259    3.2719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0549    2.4469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0549    3.2719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0549    0.7969    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.7693    1.2094    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.4838    0.7969    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4838   -0.0281    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.7693   -0.4406    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.0549   -0.0281    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7693   -1.2656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4838   -1.6781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1983   -0.4406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1983    1.2094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7693    2.0344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  1 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  6 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 18 12  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 18 23  1  0  0  0  0
 22 24  1  1  0  0  0
 24 25  1  0  0  0  0
 21 26  1  6  0  0  0
 20 27  1  1  0  0  0
 19 28  1  6  0  0  0
  2 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
  1 32  1  0  0  0  0
 32 33  1  0  0  0  0
 31 34  1  0  0  0  0
 34 35  1  0  0  0  0
 36 30  1  1  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 36 41  1  0  0  0  0
 40 42  1  1  0  0  0
 42 43  1  0  0  0  0
 39 44  1  6  0  0  0
 38 45  1  1  0  0  0
 37 46  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0076182

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C2=C(C=C1[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(=O)OC1=C(C=C([C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C(OC)=C1O)C(=O)O2

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O18/c1-41-21-7(23-17(35)15(33)13(31)11(5-29)43-23)3-9-25(19(21)37)45-28(40)10-4-8(22(42-2)20(38)26(10)46-27(9)39)24-18(36)16(34)14(32)12(6-30)44-24/h3-4,11-18,23-24,29-38H,5-6H2,1-2H3/t11-,12-,13-,14-,15+,16+,17-,18-,23+,24+/m1/s1

> <INCHI_KEY>
ORAUCQAGCNPIAZ-BQGIUCMVSA-N

> <FORMULA>
C28H32O18

> <MOLECULAR_WEIGHT>
656.546

> <EXACT_MASS>
656.15886419

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
63.0795729176314

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
8,16-dihydroxy-7,15-dimethoxy-6,14-bis[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-2,10-dioxatricyclo[10.4.0.0^{4,9}]hexadeca-1(12),4(9),5,7,13,15-hexaene-3,11-dione

> <ALOGPS_LOGP>
-0.95

> <JCHEM_LOGP>
-2.214244159333333

> <ALOGPS_LOGS>
-1.95

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.192329026906453

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.591189838017884

> <JCHEM_PKA_STRONGEST_BASIC>
-3.544058681939018

> <JCHEM_POLAR_SURFACE_AREA>
291.82

> <JCHEM_REFRACTIVITY>
146.7306

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.32e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8,16-dihydroxy-7,15-dimethoxy-6,14-bis[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-2,10-dioxatricyclo[10.4.0.0^{4,9}]hexadeca-1(12),4(9),5,7,13,15-hexaene-3,11-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       9.168   3.798   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.168   2.258   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.079   1.169   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.668  -0.254   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       6.539   1.169   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.450   2.258   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.450   3.798   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.539   4.886   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.950   6.309   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.079   4.886   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.116   4.568   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.783   3.798   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.783   2.258   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.116   1.488   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.116  -0.052   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.449   1.488   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.449  -0.052   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.449   4.568   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.115   3.798   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.218   4.568   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.218   6.108   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.115   6.878   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.449   6.108   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       0.115   8.418   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -1.218   9.188   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -2.552   6.878   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -2.552   3.798   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.115   2.258   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      10.502   1.488   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.835   2.258   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      11.835   3.798   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.502   4.568   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      10.502   6.108   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      13.169   4.568   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      13.169   6.108   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      13.169   1.488   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      14.503   2.258   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      15.836   1.488   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      15.836  -0.052   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      14.503  -0.822   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      13.169  -0.052   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      14.503  -2.362   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      15.836  -3.132   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      17.170  -0.822   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      17.170   2.258   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      14.503   3.798   0.000  0.00  0.00           O+0
CONECT    1    2   10   32                                                  
CONECT    2    1    3   29                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   14                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    1                                                       
CONECT   11    7   12                                                       
CONECT   12   11   13   18                                                  
CONECT   13   12   14   16                                                  
CONECT   14   13    6   15                                                  
CONECT   15   14                                                            
CONECT   16   13   17                                                       
CONECT   17   16                                                            
CONECT   18   12   19   23                                                  
CONECT   19   18   20   28                                                  
CONECT   20   19   21   27                                                  
CONECT   21   20   22   26                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22   18                                                       
CONECT   24   22   25                                                       
CONECT   25   24                                                            
CONECT   26   21                                                            
CONECT   27   20                                                            
CONECT   28   19                                                            
CONECT   29    2   30                                                       
CONECT   30   29   31   36                                                  
CONECT   31   30   32   34                                                  
CONECT   32   31    1   33                                                  
CONECT   33   32                                                            
CONECT   34   31   35                                                       
CONECT   35   34                                                            
CONECT   36   30   37   41                                                  
CONECT   37   36   38   46                                                  
CONECT   38   37   39   45                                                  
CONECT   39   38   40   44                                                  
CONECT   40   39   41   42                                                  
CONECT   41   40   36                                                       
CONECT   42   40   43                                                       
CONECT   43   42                                                            
CONECT   44   39                                                            
CONECT   45   38                                                            
CONECT   46   37                                                            
MASTER        0    0    0    0    0    0    0    0   46    0  100    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₂O₁₈

Average Mass

656.5460 Da

Monoisotopic Mass

656.15886 Da

IUPAC Name

8,16-dihydroxy-7,15-dimethoxy-6,14-bis[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-2,10-dioxatricyclo[10.4.0.0^{4,9}]hexadeca-1(12),4(9),5,7,13,15-hexaene-3,11-dione

Traditional Name

8,16-dihydroxy-7,15-dimethoxy-6,14-bis[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-2,10-dioxatricyclo[10.4.0.0^{4,9}]hexadeca-1(12),4(9),5,7,13,15-hexaene-3,11-dione

CAS Registry Number

Not Available

SMILES

COC1=C(O)C2=C(C=C1[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(=O)OC1=C(C=C([C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C(OC)=C1O)C(=O)O2

InChI Identifier

InChI=1S/C28H32O18/c1-41-21-7(23-17(35)15(33)13(31)11(5-29)43-23)3-9-25(19(21)37)45-28(40)10-4-8(22(42-2)20(38)26(10)46-27(9)39)24-18(36)16(34)14(32)12(6-30)44-24/h3-4,11-18,23-24,29-38H,5-6H2,1-2H3/t11-,12-,13-,14-,15+,16+,17-,18-,23+,24+/m1/s1

InChI Key

ORAUCQAGCNPIAZ-BQGIUCMVSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Ardisia japonica	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
Hexose monosaccharide
C-glycosyl compound
Anisole
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Monosaccharide
Oxane
Benzenoid
1,2-diol
Lactone
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid derivative
Oxacycle
Polyol
Organic oxide
Alcohol
Hydrocarbon derivative
Primary alcohol
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	-0.95	ALOGPS
logP	-2.2	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	9.59	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	291.82 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	146.73 m³·mol⁻¹	ChemAxon
Polarizability	63.08 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	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00038492

Chemspider ID

23283127

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44423020

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Dat NT, Bae K, Wamiru A, McMahon JB, Le Grice SF, Bona M, Beutler JA, Kim YH: A dimeric lactone from Ardisia japonica with inhibitory activity for HIV-1 and HIV-2 ribonuclease H. J Nat Prod. 2007 May;70(5):839-41. doi: 10.1021/np060359m. Epub 2007 Mar 31. [PubMed:17397219 ]
Mavlan M, Ng K, Panesar H, Yepremyan A, Minehan TG: Synthesis of 3,3'-di-O-methyl ardimerin and exploration of its DNA binding properties. Org Lett. 2014 Apr 18;16(8):2212-5. doi: 10.1021/ol500725e. Epub 2014 Apr 9. [PubMed:24712737 ]

Showing NP-Card for (+)-Ardimerin (NP0076182)

MOL for NP0076182 ((+)-Ardimerin)

3D MOL for NP0076182 ((+)-Ardimerin)

3D SDF for NP0076182 ((+)-Ardimerin)

3D-SDF for NP0076182 ((+)-Ardimerin)

PDB for NP0076182 ((+)-Ardimerin)

3D PDB for NP0076182 ((+)-Ardimerin)

SMILES for NP0076182 ((+)-Ardimerin)

INCHI for NP0076182 ((+)-Ardimerin)

Structure for NP0076182 ((+)-Ardimerin)

3D Structure for NP0076182 ((+)-Ardimerin)