NP-MRD: Showing NP-Card for (3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid (NP0165456)

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Record Information

Version

2.0

Created at

2022-09-03 00:36:27 UTC

Updated at

2022-09-03 00:36:27 UTC

NP-MRD ID

NP0165456

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid

Description

(3S)-4-{[(2S,3R,4R,5S,6R)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position. (3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid is found in Dianthus caryophyllus. Based on a literature review very few articles have been published on (3S)-4-{[(2S,3R,4R,5S,6R)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032202362D          

 39 42  0  0  1  0            999 V2000
    7.1447   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.0026   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   11.4315   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   11.4315   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309032202362D          

 39 42  0  0  1  0            999 V2000
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 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 17 23  1  0  0  0  0
 16 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  2  0  0  0  0
 25 32  1  0  0  0  0
 32 33  1  0  0  0  0
 15 33  1  0  0  0  0
 13 34  1  0  0  0  0
 34 35  1  1  0  0  0
 34 36  1  0  0  0  0
 36 37  1  6  0  0  0
 36 38  1  0  0  0  0
 11 38  1  0  0  0  0
 38 39  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0165456

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H](CC(O)=O)C(=O)OC[C@@H]1O[C@H](OC2=C(OC3=CC(O)=CC(O)=C3C2)C2=CC=C(O)C=C2)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H26O14/c26-11-3-1-10(2-4-11)23-17(7-13-14(28)5-12(27)6-16(13)37-23)38-25-22(34)21(33)20(32)18(39-25)9-36-24(35)15(29)8-19(30)31/h1-6,15,18,20-22,25-29,32-34H,7-9H2,(H,30,31)/t15-,18-,20-,21+,22-,25-/m0/s1

> <INCHI_KEY>
BUYVRDKTUIDPKL-JJWFNQQGSA-N

> <FORMULA>
C25H26O14

> <MOLECULAR_WEIGHT>
550.469

> <EXACT_MASS>
550.132255517

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
51.656259558816814

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-4-{[(2S,3R,4R,5S,6R)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid

> <ALOGPS_LOGP>
0.70

> <JCHEM_LOGP>
-0.7357400813333339

> <ALOGPS_LOGS>
-2.91

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.709295384164552

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5501397697447445

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6491034791118997

> <JCHEM_POLAR_SURFACE_AREA>
232.89999999999995

> <JCHEM_REFRACTIVITY>
127.99330000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.83e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-4-{[(2S,3R,4R,5S,6R)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  O   UNK     0      13.337  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      14.670  -3.850   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      14.670  -5.390   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      16.004  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.338  -3.850   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      17.338  -5.390   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      18.672  -3.080   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      18.672  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      20.005  -3.850   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      21.339  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      22.673  -3.850   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      24.006  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      25.340  -3.850   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      26.674  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      28.007  -3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      29.341  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      29.341  -1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.007  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      28.007   0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      29.341   1.540   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      29.341   3.080   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      30.675   0.770   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      30.675  -0.770   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      30.675  -3.850   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      30.675  -5.390   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      32.008  -6.160   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      32.008  -7.700   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      33.342  -8.470   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      30.675  -8.470   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      29.341  -7.700   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      28.007  -8.470   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      29.341  -6.160   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      28.007  -5.390   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      25.340  -5.390   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      26.674  -6.160   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      24.006  -6.160   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      24.006  -7.700   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      22.673  -5.390   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      21.339  -6.160   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   38                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   34                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   33                                                  
CONECT   16   15   17   24                                                  
CONECT   17   16   18   23                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   17                                                       
CONECT   24   16   25                                                       
CONECT   25   24   26   32                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   25   33                                                  
CONECT   33   32   15                                                       
CONECT   34   13   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   11   39                                                  
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Value	Source
(3S)-4-{[(2S,3R,4R,5S,6R)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoate	Generator

Chemical Formula

C₂₅H₂₆O₁₄

Average Mass

550.4690 Da

Monoisotopic Mass

550.13226 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

O[C@@H](CC(O)=O)C(=O)OC[C@@H]1O[C@H](OC2=C(OC3=CC(O)=CC(O)=C3C2)C2=CC=C(O)C=C2)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C25H26O14/c26-11-3-1-10(2-4-11)23-17(7-13-14(28)5-12(27)6-16(13)37-23)38-25-22(34)21(33)20(32)18(39-25)9-36-24(35)15(29)8-19(30)31/h1-6,15,18,20-22,25-29,32-34H,7-9H2,(H,30,31)/t15-,18-,20-,21+,22-,25-/m0/s1

InChI Key

BUYVRDKTUIDPKL-JJWFNQQGSA-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
Dianthus caryophyllus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid-3-O-glycosides

Alternative Parents

Substituents

Flavonoid-3-o-glycoside
Saccharolipid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Beta-hydroxy acid
Fatty acid ester
Phenol
Monocyclic benzene moiety
Fatty acyl
Dicarboxylic acid or derivatives
Benzenoid
Hydroxy acid
Monosaccharide
Oxane
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Carboxylic acid
Carboxylic acid derivative
Oxacycle
Acetal
Polyol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Alcohol
Organooxygen compound
Organic oxygen 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	0.7	ALOGPS
logS	-2.9	ALOGPS

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

162872620

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid (NP0165456)

MOL for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

3D MOL for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

3D SDF for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

3D-SDF for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

PDB for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

3D PDB for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

SMILES for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

INCHI for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

Structure for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)

3D Structure for NP0165456 ((3s)-4-{[(2s,3r,4r,5s,6r)-6-{[5,7-dihydroxy-2-(4-hydroxyphenyl)-4h-chromen-3-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-4-oxobutanoic acid)