NP-MRD: Showing NP-Card for [(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate (NP0330213)

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Record Information

Version

2.0

Created at

2022-09-12 15:21:14 UTC

Updated at

2022-09-12 15:21:14 UTC

NP-MRD ID

NP0330213

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate

Description

CHEMBL575364 belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. [(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate is found in Fridericia patellifera. Based on a literature review very few articles have been published on CHEMBL575364.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122217212D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309122217212D          

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   -0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    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
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
  5 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  2  0  0  0  0
 24 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 22 34  1  0  0  0  0
 34 35  2  0  0  0  0
 18 35  1  0  0  0  0
 35 36  1  0  0  0  0
 16 37  1  0  0  0  0
 37 38  1  1  0  0  0
 37 39  1  0  0  0  0
 39 40  1  6  0  0  0
 39 41  1  0  0  0  0
 14 41  1  0  0  0  0
 41 42  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0330213

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H](COC(=O)\C=C\C2=CC=C(O)C=C2)O[C@@H](OC2=C(O)C=C3OC4=CC(O)=C(O)C=C4C(=O)C3=C2O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C28H24O14/c29-12-4-1-11(2-5-12)3-6-20(33)39-10-19-23(35)25(37)26(38)28(41-19)42-27-16(32)9-18-21(24(27)36)22(34)13-7-14(30)15(31)8-17(13)40-18/h1-9,19,23,25-26,28-32,35-38H,10H2/b6-3+/t19-,23-,25+,26-,28+/m1/s1

> <INCHI_KEY>
LKAUZCQGGQBXJB-KSSKDEGSSA-N

> <FORMULA>
C28H24O14

> <MOLECULAR_WEIGHT>
584.486

> <EXACT_MASS>
584.116605453

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
56.11829171254085

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxy]oxan-2-yl]methyl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_LOGP>
2.554070915

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.075663641220075

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.39096066675708

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6491103301377654

> <JCHEM_POLAR_SURFACE_AREA>
232.89999999999998

> <JCHEM_REFRACTIVITY>
140.4138

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335 -13.860   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001 -14.630   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001 -16.170   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335 -16.940   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335 -18.480   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001 -19.250   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.001 -20.790   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667 -18.480   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667 -16.940   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.001 -11.550   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10    5                                                       
CONECT   12    2   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   41                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   37                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   35                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23   34                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   31                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   24   32                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   22   35                                                  
CONECT   35   34   18   36                                                  
CONECT   36   35                                                            
CONECT   37   16   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   14   42                                                  
CONECT   42   41                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   92    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₂₄O₁₄

Average Mass

584.4860 Da

Monoisotopic Mass

584.11661 Da

IUPAC Name

[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxy]oxan-2-yl]methyl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

Traditional Name

[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](COC(=O)\C=C\C2=CC=C(O)C=C2)O[C@@H](OC2=C(O)C=C3OC4=CC(O)=C(O)C=C4C(=O)C3=C2O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C28H24O14/c29-12-4-1-11(2-5-12)3-6-20(33)39-10-19-23(35)25(37)26(38)28(41-19)42-27-16(32)9-18-21(24(27)36)22(34)13-7-14(30)15(31)8-17(13)40-18/h1-9,19,23,25-26,28-32,35-38H,10H2/b6-3+/t19-,23-,25+,26-,28+/m1/s1

InChI Key

LKAUZCQGGQBXJB-KSSKDEGSSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Fridericia patellifera	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Phenolic glycoside
Xanthone
Coumaric acid ester
Cinnamic acid or derivatives
Coumaric acid or derivatives
Hydroxycinnamic acid or derivatives
Cinnamic acid ester
Chromone
O-glycosyl compound
Glycosyl compound
Styrene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Fatty acid ester
Pyranone
Monosaccharide
Pyran
Benzenoid
Fatty acyl
Monocyclic benzene moiety
Oxane
Heteroaromatic compound
Vinylogous acid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Secondary alcohol
Oxacycle
Acetal
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Polyol
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
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	2.55	ChemAxon
pKa (Strongest Acidic)	7.39	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	232.9 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	140.41 m³·mol⁻¹	ChemAxon
Polarizability	56.12 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

Not Available

Chemspider ID

24635706

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45481963

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate (NP0330213)

MOL for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D MOL for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D SDF for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D-SDF for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

PDB for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D PDB for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

SMILES for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

INCHI for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

Structure for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D Structure for NP0330213 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)