NP-MRD: Showing NP-Card for Decumbeside B (NP0064656)

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Record Information

Version

2.0

Created at

2022-04-28 08:51:07 UTC

Updated at

2022-04-28 08:51:07 UTC

NP-MRD ID

NP0064656

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Decumbeside B

Description

(2S,3R,4S,5S,6R)-4,5-dihydroxy-2-{[(1S,2R,4S,6R,10S)-6-hydroxy-2-methyl-3,9-dioxatricyclo[4.4.0.0²,⁴]Dec-7-en-10-yl]oxy}-6-(hydroxymethyl)oxan-3-yl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate belongs to the class of organic compounds known as coumaric acid esters. These are aromatic compounds containing an ester derivative of coumaric acid. Decumbeside B is found in Ajuga decumbens . Based on a literature review very few articles have been published on (2S,3R,4S,5S,6R)-4,5-dihydroxy-2-{[(1S,2R,4S,6R,10S)-6-hydroxy-2-methyl-3,9-dioxatricyclo[4.4.0.0²,⁴]Dec-7-en-10-yl]oxy}-6-(hydroxymethyl)oxan-3-yl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282210512D          

 35 39  0  0  1  0            999 V2000
    0.7327   -1.5964    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5364   -0.7950    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1323   -0.2244    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9243   -0.4551    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1206   -1.2564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5248   -1.8271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9360    0.5769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5318    1.1475    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3356    1.9488    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9314    2.5194    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7235    2.2887    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9198    1.4874    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3239    0.9168    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7119    1.2567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9081    0.4554    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3194    2.8594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.5435    2.1795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3473    2.9809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9431    3.5515    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4448    3.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6411    4.0129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1038   -0.8455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3117    0.0906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8441   -2.4138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
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  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
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 14 15  1  0  0  0  0
 11 16  1  6  0  0  0
 10 17  1  1  0  0  0
  9 18  1  6  0  0  0
 18 19  1  0  0  0  0
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  1 35  1  1  0  0  0
M  END

     RDKit          3D

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   -0.7364    1.0513   -0.6391 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9256    1.3763   -2.0031 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4529    3.1153   -3.5289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7750    4.4710   -3.5376 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2368    3.6395   -1.4867 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9083    4.8198   -1.0983 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4650    3.1245   -0.2667 C   0  0  2  0  0  0  0  0  0  0  0  0
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 11 35  1  0
  4  2  1  0
 35  6  1  0
 35  2  1  0
 22 13  1  0
 34 28  1  0
  1 36  1  0
  1 37  1  0
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  4 39  1  6
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  7 42  1  0
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 11 45  1  1
 13 46  1  1
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 29 58  1  0
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 35 63  1  6
M  END


  Mrv1652304282210512D          

 35 39  0  0  1  0            999 V2000
    0.7327   -1.5964    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
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  1  6  1  0  0  0  0
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  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 14 15  1  0  0  0  0
 11 16  1  6  0  0  0
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  9 18  1  6  0  0  0
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 19 20  2  0  0  0  0
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 27 28  2  0  0  0  0
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 26 29  1  0  0  0  0
  2 30  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
  1 32  1  0  0  0  0
 31 33  1  6  0  0  0
 30 33  1  0  0  0  0
 30 34  1  1  0  0  0
  1 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0064656

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]12O[C@H]1C[C@@]1(O)C=CO[C@@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3OC(=O)\C=C/C3=CC=C(O)C=C3)[C@H]21

> <INCHI_IDENTIFIER>
InChI=1S/C24H28O11/c1-23-15(35-23)10-24(30)8-9-31-22(20(23)24)34-21-19(18(29)17(28)14(11-25)32-21)33-16(27)7-4-12-2-5-13(26)6-3-12/h2-9,14-15,17-22,25-26,28-30H,10-11H2,1H3/b7-4-/t14-,15+,17-,18+,19-,20-,21+,22+,23+,24+/m1/s1

> <INCHI_KEY>
DUSNEDXMOOGSOE-CMSDINTISA-N

> <FORMULA>
C24H28O11

> <MOLECULAR_WEIGHT>
492.477

> <EXACT_MASS>
492.163161722

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
48.126087898936

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-4,5-dihydroxy-2-{[(1S,2R,4S,6R,10S)-6-hydroxy-2-methyl-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl]oxy}-6-(hydroxymethyl)oxan-3-yl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate

> <ALOGPS_LOGP>
0.65

> <JCHEM_LOGP>
-0.0748284073333328

> <ALOGPS_LOGS>
-2.54

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.657135578380569

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.398328290022011

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810854075406814

> <JCHEM_POLAR_SURFACE_AREA>
167.67

> <JCHEM_REFRACTIVITY>
117.24240000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-4,5-dihydroxy-2-{[(1S,2R,4S,6R,10S)-6-hydroxy-2-methyl-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl]oxy}-6-(hydroxymethyl)oxan-3-yl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate

> <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       1.368  -2.980   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.001  -1.484   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.114  -0.419   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.592  -0.850   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.958  -2.345   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.846  -3.411   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.747   1.077   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.859   2.142   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.493   3.638   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.605   4.703   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.084   4.272   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.450   2.777   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.338   1.711   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.929   2.346   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.295   0.850   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       6.196   5.337   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.239   6.199   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.015   4.068   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.648   5.564   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.760   6.629   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -0.830   5.995   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.197   7.491   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.084   8.556   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.451  10.052   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.661  11.117   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.140  10.686   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.506   9.190   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.394   8.125   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       3.252  11.751   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -0.534  -1.370   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.117  -2.796   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       0.058  -3.790   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -2.060  -1.578   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -0.582   0.169   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       1.576  -4.506   0.000  0.00  0.00           O+0
CONECT    1    2    6   32   35                                             
CONECT    2    1    3   30                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    3    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10   18                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12   16                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12    8                                                       
CONECT   14   12   15                                                       
CONECT   15   14                                                            
CONECT   16   11                                                            
CONECT   17   10                                                            
CONECT   18    9   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27   23                                                       
CONECT   29   26                                                            
CONECT   30    2   31   33   34                                             
CONECT   31   30   32   33                                                  
CONECT   32   31    1                                                       
CONECT   33   31   30                                                       
CONECT   34   30                                                            
CONECT   35    1                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Value	Source
(2S,3R,4S,5S,6R)-4,5-Dihydroxy-2-{[(1S,2R,4S,6R,10S)-6-hydroxy-2-methyl-3,9-dioxatricyclo[4.4.0.0,]dec-7-en-10-yl]oxy}-6-(hydroxymethyl)oxan-3-yl (2Z)-3-(4-hydroxyphenyl)prop-2-enoic acid	Generator

Chemical Formula

C₂₄H₂₈O₁₁

Average Mass

492.4770 Da

Monoisotopic Mass

492.16316 Da

IUPAC Name

(2S,3R,4S,5S,6R)-4,5-dihydroxy-2-{[(1S,2R,4S,6R,10S)-6-hydroxy-2-methyl-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl]oxy}-6-(hydroxymethyl)oxan-3-yl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate

Traditional Name

(2S,3R,4S,5S,6R)-4,5-dihydroxy-2-{[(1S,2R,4S,6R,10S)-6-hydroxy-2-methyl-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl]oxy}-6-(hydroxymethyl)oxan-3-yl (2Z)-3-(4-hydroxyphenyl)prop-2-enoate

CAS Registry Number

Not Available

SMILES

C[C@]12O[C@H]1C[C@@]1(O)C=CO[C@@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3OC(=O)\C=C/C3=CC=C(O)C=C3)[C@H]21

InChI Identifier

InChI=1S/C24H28O11/c1-23-15(35-23)10-24(30)8-9-31-22(20(23)24)34-21-19(18(29)17(28)14(11-25)32-21)33-16(27)7-4-12-2-5-13(26)6-3-12/h2-9,14-15,17-22,25-26,28-30H,10-11H2,1H3/b7-4-/t14-,15+,17-,18+,19-,20-,21+,22+,23+,24+/m1/s1

InChI Key

DUSNEDXMOOGSOE-CMSDINTISA-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
Ajuga decumbens	Plant	KNApSAcK

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
Cinnamic acid ester
Hexose monosaccharide
Coumaric acid or derivatives
O-glycosyl compound
Glycosyl compound
Styrene
1-hydroxy-2-unsubstituted benzenoid
Phenol
Fatty acid ester
Fatty acyl
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
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	0.65	ALOGPS
logP	-0.075	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	9.4	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	167.67 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	117.24 m³·mol⁻¹	ChemAxon
Polarizability	48.13 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

162982065

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Decumbeside B (NP0064656)

MOL for NP0064656 (Decumbeside B)

3D MOL for NP0064656 (Decumbeside B)

3D SDF for NP0064656 (Decumbeside B)

3D-SDF for NP0064656 (Decumbeside B)

PDB for NP0064656 (Decumbeside B)

3D PDB for NP0064656 (Decumbeside B)

SMILES for NP0064656 (Decumbeside B)

INCHI for NP0064656 (Decumbeside B)

Structure for NP0064656 (Decumbeside B)

3D Structure for NP0064656 (Decumbeside B)