NP-MRD: Showing NP-Card for 5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl (NP0244451)

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Record Information

Version

2.0

Created at

2022-09-07 05:15:17 UTC

Updated at

2022-09-07 05:15:17 UTC

NP-MRD ID

NP0244451

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl

Description

5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl is found in Lonicera japonica.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072207152D          

 37 39  0  0  1  0            999 V2000
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M  RAD  1  18   2
M  END

     RDKit          3D

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M  RAD  1  18   2
M  END


  Mrv1652309072207152D          

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 24 25  1  0  0  0  0
  3 25  1  0  0  0  0
 25 26  1  1  0  0  0
 27 26  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  6  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  0  0  0  0
 34 35  1  6  0  0  0
 34 36  1  0  0  0  0
 27 36  1  0  0  0  0
 36 37  1  1  0  0  0
M  RAD  1  18   2
M  END
> <DATABASE_ID>
NP0244451

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCCN1[CH]C(\C=C\[C@H]2[C@H](C=C)[C@@H](O[C@@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)OC=C2C(O)=O)=CC(=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H30NO12/c1-2-14-15(4-3-12-7-13(21(31)32)9-25(8-12)5-6-26)16(22(33)34)11-35-23(14)37-24-20(30)19(29)18(28)17(10-27)36-24/h2-4,7-9,11,14-15,17-20,23-24,26-30H,1,5-6,10H2,(H,31,32)(H,33,34)/b4-3+/t14-,15-,17+,18-,19-,20+,23+,24-/m0/s1

> <INCHI_KEY>
AXKDRDXXIFCZRJ-WMAQMIOOSA-N

> <FORMULA>
C24H30NO12

> <MOLECULAR_WEIGHT>
524.499

> <EXACT_MASS>
524.17680041

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
50.78285062303081

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-carboxy-3-[(E)-2-[(2R,3S,4S)-5-carboxy-3-ethenyl-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-1,2-dihydropyridin-2-yl

> <JCHEM_LOGP>
-2.994655555951666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.305903792753335

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.500355599090116

> <JCHEM_PKA_STRONGEST_BASIC>
5.294770075171564

> <JCHEM_POLAR_SURFACE_AREA>
206.67999999999998

> <JCHEM_REFRACTIVITY>
127.59150000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
5-carboxy-3-[(E)-2-[(2R,3S,4S)-5-carboxy-3-ethenyl-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2H-pyridin-2-yl

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -2.667  -0.000   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   25                                                  
CONECT    4    3    5   19                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    9   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   14    7                                                       
CONECT   19    4   20   23                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   19   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24    3   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   36                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   27   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₀NO₁₂

Average Mass

524.4990 Da

Monoisotopic Mass

524.17680 Da

IUPAC Name

5-carboxy-3-[(E)-2-[(2R,3S,4S)-5-carboxy-3-ethenyl-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-1,2-dihydropyridin-2-yl

Traditional Name

5-carboxy-3-[(E)-2-[(2R,3S,4S)-5-carboxy-3-ethenyl-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2H-pyridin-2-yl

CAS Registry Number

Not Available

SMILES

OCCN1[CH]C(\C=C\[C@H]2[C@H](C=C)[C@@H](O[C@@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)OC=C2C(O)=O)=CC(=C1)C(O)=O

InChI Identifier

InChI=1S/C24H30NO12/c1-2-14-15(4-3-12-7-13(21(31)32)9-25(8-12)5-6-26)16(22(33)34)11-35-23(14)37-24-20(30)19(29)18(28)17(10-27)36-24/h2-4,7-9,11,14-15,17-20,23-24,26-30H,1,5-6,10H2,(H,31,32)(H,33,34)/b4-3+/t14-,15-,17+,18-,19-,20+,23+,24-/m0/s1

InChI Key

AXKDRDXXIFCZRJ-WMAQMIOOSA-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
Lonicera japonica	LOTUS Database	35616633

Chemical Taxonomy

Classification

Not classified

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	-3	ChemAxon
pKa (Strongest Acidic)	3.5	ChemAxon
pKa (Strongest Basic)	5.29	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	206.68 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	127.59 m³·mol⁻¹	ChemAxon
Polarizability	50.78 Å³	ChemAxon
Number of Rings	3	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

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl (NP0244451)

MOL for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

3D MOL for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

3D SDF for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

3D-SDF for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

PDB for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

3D PDB for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

SMILES for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

INCHI for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

Structure for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)

3D Structure for NP0244451 (5-carboxy-3-[(1e)-2-[(2r,3s,4s)-5-carboxy-3-ethenyl-2-{[(2s,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2h-pyran-4-yl]ethenyl]-1-(2-hydroxyethyl)-2h-pyridin-2-yl)