NP-MRD: Showing NP-Card for kodemarioside D (NP0039397)

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Record Information

Version

2.0

Created at

2021-06-20 21:50:31 UTC

Updated at

2021-06-30 00:12:42 UTC

NP-MRD ID

NP0039397

Secondary Accession Numbers

None

Natural Product Identification

Common Name

kodemarioside D

Provided By

JEOL Database JEOL Logo

Description

Kodemarioside B belongs to the class of organic compounds known as coumaric acid esters. These are aromatic compounds containing an ester derivative of coumaric acid. kodemarioside D is found in Spiraea cantoniensis. kodemarioside D was first documented in 2010 (Yoshida, K. et al.). Based on a literature review very few articles have been published on Kodemarioside B.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202123503D          

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M  END

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M  END


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  7  6  1  0  0  0  0
  6  5  1  0  0  0  0
  5 35  1  0  0  0  0
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  9 10  2  0  0  0  0
 21 20  2  0  0  0  0
  7  8  2  0  0  0  0
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  5  4  1  0  0  0  0
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  4  2  2  3  0  0  0
 25 27  2  0  0  0  0
  2  1  1  0  0  0  0
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  2  3  1  0  0  0  0
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M  END
> <DATABASE_ID>
NP0039397

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C([H])=C(\C([H])=C(\[H])C(=O)OC([H])([H])[C@@]2([H])O[C@@]([H])(OC([H])([H])C(\[H])=C3\C(=O)O[C@]([H])(C([H])=C(C([H])([H])[H])C([H])([H])[H])[C@@]3([H])O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]2([H])O[H])C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C25H30O11/c1-13(2)11-17-20(28)16(24(32)35-17)9-10-33-25-23(31)22(30)21(29)18(36-25)12-34-19(27)8-5-14-3-6-15(26)7-4-14/h3-9,11,17-18,20-23,25-26,28-31H,10,12H2,1-2H3/b8-5-,16-9+/t17-,18-,20+,21-,22+,23-,25-/m1/s1

> <INCHI_KEY>
KRHXGSVJPFGCQY-APJRQFEFSA-N

> <FORMULA>
C25H30O11

> <MOLECULAR_WEIGHT>
506.504

> <EXACT_MASS>
506.178811786

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
49.74406054100243

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{2-[(3E,4S,5R)-4-hydroxy-5-(2-methylprop-1-en-1-yl)-2-oxooxolan-3-ylidene]ethoxy}oxan-2-yl]methyl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate

> <ALOGPS_LOGP>
1.04

> <JCHEM_LOGP>
1.4015628896666663

> <ALOGPS_LOGS>
-3.07

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.172778373002481

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.397913286918456

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5738051240834325

> <JCHEM_POLAR_SURFACE_AREA>
172.20999999999998

> <JCHEM_REFRACTIVITY>
126.09200000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.31e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{2-[(3E,4S,5R)-4-hydroxy-5-(2-methylprop-1-en-1-yl)-2-oxooxolan-3-ylidene]ethoxy}oxan-2-yl]methyl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 66 68  0  0  0  0  0  0  0  0999 V2000
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M  END

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0       1.386  -0.434  -5.880  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.053  -1.900  -5.931  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.626  -2.626  -7.120  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.319  -2.557  -5.011  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.351  -1.982  -3.788  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.612  -2.643  -3.636  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.902  -2.750  -2.315  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.993  -3.047  -1.858  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.679  -2.465  -1.523  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.749  -2.468  -0.179  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.307  -2.206   0.851  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.442  -1.609   0.247  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.566  -1.551   1.128  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.230  -0.840   2.307  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.313  -0.702   3.235  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.786   0.051   4.469  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.359   1.381   4.113  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.054   1.518   3.763  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.176   0.677   3.824  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.885   2.911   3.303  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.231   3.297   2.197  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.437   2.446   1.208  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.601   1.734   1.519  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.266   0.997   0.534  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.764   0.980  -0.763  0.00  0.00           C+0
HETATM   26  O   UNK     0      -2.388   0.290  -1.760  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.603   1.672  -1.086  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.059   2.408  -0.101  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.502   0.024   2.587  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.631   0.030   3.465  0.00  0.00           O+0
HETATM   31  C   UNK     0       4.895  -0.671   1.280  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.921   0.098   0.630  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.683  -0.819   0.366  0.00  0.00           C+0
HETATM   34  O   UNK     0       4.074  -1.524  -0.823  0.00  0.00           O+0
HETATM   35  C   UNK     0       0.426  -2.243  -2.499  0.00  0.00           C+0
HETATM   36  O   UNK     0       1.284  -1.145  -2.203  0.00  0.00           O+0
HETATM   37  H   UNK     0       2.470  -0.293  -5.947  0.00  0.00           H+0
HETATM   38  H   UNK     0       1.059   0.053  -4.958  0.00  0.00           H+0
HETATM   39  H   UNK     0       0.917   0.088  -6.720  0.00  0.00           H+0
HETATM   40  H   UNK     0       1.359  -3.688  -7.128  0.00  0.00           H+0
HETATM   41  H   UNK     0       1.252  -2.183  -8.050  0.00  0.00           H+0
HETATM   42  H   UNK     0       2.719  -2.557  -7.116  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.160  -3.627  -5.146  0.00  0.00           H+0
HETATM   44  H   UNK     0      -0.561  -0.915  -3.928  0.00  0.00           H+0
HETATM   45  H   UNK     0      -1.717  -2.692   0.274  0.00  0.00           H+0
HETATM   46  H   UNK     0       0.576  -3.152   1.335  0.00  0.00           H+0
HETATM   47  H   UNK     0      -0.101  -1.523   1.605  0.00  0.00           H+0
HETATM   48  H   UNK     0       2.869  -2.579   1.368  0.00  0.00           H+0
HETATM   49  H   UNK     0       3.621  -1.702   3.567  0.00  0.00           H+0
HETATM   50  H   UNK     0       3.574   0.155   5.222  0.00  0.00           H+0
HETATM   51  H   UNK     0       1.962  -0.503   4.937  0.00  0.00           H+0
HETATM   52  H   UNK     0       1.388   3.653   3.914  0.00  0.00           H+0
HETATM   53  H   UNK     0       0.215   4.357   1.950  0.00  0.00           H+0
HETATM   54  H   UNK     0      -2.001   1.751   2.530  0.00  0.00           H+0
HETATM   55  H   UNK     0      -3.168   0.454   0.797  0.00  0.00           H+0
HETATM   56  H   UNK     0      -3.188  -0.133  -1.399  0.00  0.00           H+0
HETATM   57  H   UNK     0      -0.220   1.648  -2.102  0.00  0.00           H+0
HETATM   58  H   UNK     0       0.957   2.960  -0.369  0.00  0.00           H+0
HETATM   59  H   UNK     0       4.252   1.070   2.371  0.00  0.00           H+0
HETATM   60  H   UNK     0       6.372   0.371   2.924  0.00  0.00           H+0
HETATM   61  H   UNK     0       5.346  -1.650   1.486  0.00  0.00           H+0
HETATM   62  H   UNK     0       5.991  -0.283  -0.270  0.00  0.00           H+0
HETATM   63  H   UNK     0       3.343   0.173   0.040  0.00  0.00           H+0
HETATM   64  H   UNK     0       3.277  -1.541  -1.396  0.00  0.00           H+0
HETATM   65  H   UNK     0       1.038  -3.151  -2.565  0.00  0.00           H+0
HETATM   66  H   UNK     0       1.122  -0.917  -1.264  0.00  0.00           H+0
CONECT    1    2   37   38   39                                             
CONECT    2    4    1    3                                                  
CONECT    3    2   40   41   42                                             
CONECT    4    5    2   43                                                  
CONECT    5    6   35    4   44                                             
CONECT    6    7    5                                                       
CONECT    7    9    6    8                                                  
CONECT    8    7                                                            
CONECT    9    7   35   10                                                  
CONECT   10    9   11   45                                                  
CONECT   11   10   12   46   47                                             
CONECT   12   11   13                                                       
CONECT   13   14   33   12   48                                             
CONECT   14   15   13                                                       
CONECT   15   29   14   16   49                                             
CONECT   16   17   15   50   51                                             
CONECT   17   16   18                                                       
CONECT   18   19   20   17                                                  
CONECT   19   18                                                            
CONECT   20   21   18   52                                                  
CONECT   21   20   22   53                                                  
CONECT   22   28   23   21                                                  
CONECT   23   24   22   54                                                  
CONECT   24   23   25   55                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25   56                                                       
CONECT   27   28   25   57                                                  
CONECT   28   27   22   58                                                  
CONECT   29   31   15   30   59                                             
CONECT   30   29   60                                                       
CONECT   31   33   29   32   61                                             
CONECT   32   31   62                                                       
CONECT   33   31   34   13   63                                             
CONECT   34   33   64                                                       
CONECT   35    5    9   36   65                                             
CONECT   36   35   66                                                       
CONECT   37    1                                                            
CONECT   38    1                                                            
CONECT   39    1                                                            
CONECT   40    3                                                            
CONECT   41    3                                                            
CONECT   42    3                                                            
CONECT   43    4                                                            
CONECT   44    5                                                            
CONECT   45   10                                                            
CONECT   46   11                                                            
CONECT   47   11                                                            
CONECT   48   13                                                            
CONECT   49   15                                                            
CONECT   50   16                                                            
CONECT   51   16                                                            
CONECT   52   20                                                            
CONECT   53   21                                                            
CONECT   54   23                                                            
CONECT   55   24                                                            
CONECT   56   26                                                            
CONECT   57   27                                                            
CONECT   58   28                                                            
CONECT   59   29                                                            
CONECT   60   30                                                            
CONECT   61   31                                                            
CONECT   62   32                                                            
CONECT   63   33                                                            
CONECT   64   34                                                            
CONECT   65   35                                                            
CONECT   66   36                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  136    0
END

RDKit          3D

66 68  0  0  0  0  0  0  0  0999 V2000
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 36 66  1  0
 11 46  1  0
 11 47  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₀O₁₁

Average Mass

506.5040 Da

Monoisotopic Mass

506.17881 Da

IUPAC Name

[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{2-[(3E,4S,5R)-4-hydroxy-5-(2-methylprop-1-en-1-yl)-2-oxooxolan-3-ylidene]ethoxy}oxan-2-yl]methyl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate

Traditional Name

[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{2-[(3E,4S,5R)-4-hydroxy-5-(2-methylprop-1-en-1-yl)-2-oxooxolan-3-ylidene]ethoxy}oxan-2-yl]methyl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate

CAS Registry Number

Not Available

SMILES

[H]OC1=C([H])C([H])=C(\C([H])=C(\[H])C(=O)OC([H])([H])[C@@]2([H])O[C@@]([H])(OC([H])([H])C(\[H])=C3\C(=O)O[C@]([H])(C([H])=C(C([H])([H])[H])C([H])([H])[H])[C@@]3([H])O[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]2([H])O[H])C([H])=C1[H]

InChI Identifier

InChI=1S/C25H30O11/c1-13(2)11-17-20(28)16(24(32)35-17)9-10-33-25-23(31)22(30)21(29)18(36-25)12-34-19(27)8-5-14-3-6-15(26)7-4-14/h3-9,11,17-18,20-23,25-26,28-31H,10,12H2,1-2H3/b8-5-,16-9+/t17-,18-,20+,21-,22+,23-,25-/m1/s1

InChI Key

KRHXGSVJPFGCQY-APJRQFEFSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, acetone-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
Spiraea cantoniensis	JEOL database	Yoshida, K. et al, J. Nat. Prod. 73, 814 (2010)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumaric acid esters. These are aromatic compounds containing an ester derivative of coumaric acid.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Cinnamic acids and derivatives

Sub Class

Hydroxycinnamic acids and derivatives

Direct Parent

Coumaric acid esters

Alternative Parents

Substituents

Coumaric acid ester
Coumaric acid or derivatives
Cinnamic acid ester
Glycosyl compound
O-glycosyl compound
Styrene
1-hydroxy-2-unsubstituted benzenoid
Fatty acid ester
Phenol
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Gamma butyrolactone
Monosaccharide
Fatty acyl
Oxane
Benzenoid
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Oxolane
Carboxylic acid ester
Secondary alcohol
Lactone
Carboxylic acid derivative
Acetal
Polyol
Organoheterocyclic compound
Oxacycle
Carbonyl group
Organooxygen compound
Organic oxygen compound
Organic oxide
Alcohol
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	1.04	ALOGPS
logP	1.4	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	9.4	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	172.21 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	126.09 m³·mol⁻¹	ChemAxon
Polarizability	49.74 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46833998

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yoshida, K. et al. (2010). Yoshida, K. et al, J. Nat. Prod. 73, 814 (2010). J. Nat. Prod..

Showing NP-Card for kodemarioside D (NP0039397)

MOL for NP0039397 (kodemarioside D)

3D MOL for NP0039397 (kodemarioside D)

3D SDF for NP0039397 (kodemarioside D)

3D-SDF for NP0039397 (kodemarioside D)

PDB for NP0039397 (kodemarioside D)

3D PDB for NP0039397 (kodemarioside D)

SMILES for NP0039397 (kodemarioside D)

INCHI for NP0039397 (kodemarioside D)

Structure for NP0039397 (kodemarioside D)

3D Structure for NP0039397 (kodemarioside D)