NP-MRD: Showing NP-Card for 4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid (NP0327297)

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Record Information

Version

2.0

Created at

2022-09-12 09:45:20 UTC

Updated at

2022-09-12 09:45:20 UTC

NP-MRD ID

NP0327297

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid

Description

CHEMBL3188552 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. 4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid is found in Chenopodium formosanum. CHEMBL3188552 is a moderately basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004191513512D          

 39 42  0  0  0  0            999 V2000
    4.9279    3.5854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4990    1.9354    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4990    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.1435    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    2.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2135   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.6424    2.3479    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
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  3 38  1  0  0  0  0
 38 39  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1533004191513512D          

 39 42  0  0  0  0            999 V2000
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 17 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 12 27  1  0  0  0  0
  9 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
  7 29  1  0  0  0  0
 29 30  1  0  0  0  0
 11 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
  5 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
  3 38  1  0  0  0  0
 38 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0327297

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2=CC3=C(C=C2O)N(C=CC2=CC(=NC(C2)C(O)=O)C(O)=O)C(C3)C(O)=O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H26N2O13/c27-8-17-18(29)19(30)20(31)24(39-17)38-16-6-10-5-14(23(36)37)26(13(10)7-15(16)28)2-1-9-3-11(21(32)33)25-12(4-9)22(34)35/h1-3,6-7,12,14,17-20,24,27-31H,4-5,8H2,(H,32,33)(H,34,35)(H,36,37)

> <INCHI_KEY>
CTMLKIKAUFEMLE-UHFFFAOYSA-N

> <FORMULA>
C24H26N2O13

> <MOLECULAR_WEIGHT>
550.473

> <EXACT_MASS>
550.143488905

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
53.02165436208586

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1H-indol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid

> <ALOGPS_LOGP>
-0.38

> <JCHEM_LOGP>
-1.4741221813378542

> <ALOGPS_LOGS>
-2.72

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.524085393891348

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.953347859884144

> <JCHEM_PKA_STRONGEST_BASIC>
2.2488332110015534

> <JCHEM_POLAR_SURFACE_AREA>
247.10999999999993

> <JCHEM_REFRACTIVITY>
127.73879999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.04e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  O   UNK     0       9.199   6.693   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.865   5.923   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.865   4.383   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.531   3.613   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.531   2.073   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.198   1.303   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.268   1.597   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -0.268   4.089   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -0.744   5.553   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.287   6.698   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.189   8.162   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.696   8.483   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.171   9.947   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      -1.141  11.092   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       0.365  10.771   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.841   9.307   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.396  11.916   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.920  13.381   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       2.902  11.596   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -3.678  10.267   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -4.154  11.732   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -4.708   9.123   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.198   4.383   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -2.713   2.843   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -3.483   4.177   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -3.483   1.509   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       7.865   1.303   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       7.865  -0.237   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       9.199   2.073   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      10.533   1.303   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       9.199   3.613   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      10.533   4.383   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   38                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   34                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   29                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   27                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   31                                                  
CONECT   12   11   13   27                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   24                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19   15                                                       
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   17   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   12    9   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28    7   30                                                  
CONECT   30   29                                                            
CONECT   31   11   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34    5   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36    3   39                                                  
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₆N₂O₁₃

Average Mass

550.4730 Da

Monoisotopic Mass

550.14349 Da

IUPAC Name

4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1H-indol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid

Traditional Name

4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2=CC3=C(C=C2O)N(C=CC2=CC(=NC(C2)C(O)=O)C(O)=O)C(C3)C(O)=O)C(O)C(O)C1O

InChI Identifier

InChI=1S/C24H26N2O13/c27-8-17-18(29)19(30)20(31)24(39-17)38-16-6-10-5-14(23(36)37)26(13(10)7-15(16)28)2-1-9-3-11(21(32)33)25-12(4-9)22(34)35/h1-3,6-7,12,14,17-20,24,27-31H,4-5,8H2,(H,32,33)(H,34,35)(H,36,37)

InChI Key

CTMLKIKAUFEMLE-UHFFFAOYSA-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
Chenopodium formosanum	LOTUS Database	35616633

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
Indolecarboxylic acid derivative
Indolecarboxylic acid
Hexose monosaccharide
O-glycosyl compound
Alpha-amino acid
Alpha-amino acid or derivatives
Dihydropyridinecarboxylic acid derivative
Tricarboxylic acid or derivatives
Indole or derivatives
Tertiary aliphatic/aromatic amine
1-hydroxy-2-unsubstituted benzenoid
Dihydropyridine
Aralkylamine
Monosaccharide
Hydropyridine
Oxane
Benzenoid
Secondary alcohol
Amino acid
Tertiary amine
Amino acid or derivatives
Ketimine
Acetal
Carboxylic acid derivative
Carboxylic acid
Allylamine
Enamine
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Hydrocarbon derivative
Amine
Organic oxide
Imine
Carbonyl group
Alcohol
Organic nitrogen compound
Primary alcohol
Organopnictogen compound
Organonitrogen 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	-0.38	ALOGPS
logP	-1.5	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	2.95	ChemAxon
pKa (Strongest Basic)	2.25	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	247.11 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	127.74 m³·mol⁻¹	ChemAxon
Polarizability	53.02 Å³	ChemAxon
Number of Rings	4	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

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

73265364

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid (NP0327297)

MOL for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

3D MOL for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

3D SDF for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

3D-SDF for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

PDB for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

3D PDB for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

SMILES for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

INCHI for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

Structure for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)

3D Structure for NP0327297 (4-[2-(2-carboxy-6-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydroindol-1-yl)ethenyl]-2,3-dihydropyridine-2,6-dicarboxylic acid)