NP-MRD: Showing NP-Card for methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate (NP0245199)

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Record Information

Version

2.0

Created at

2022-09-07 06:11:15 UTC

Updated at

2022-09-07 06:11:15 UTC

NP-MRD ID

NP0245199

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate

Description

MEGxp0_000012 belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate is found in Chimarrhis turbinata, Ochrosia moorei and Strychnos mellodora. Based on a literature review very few articles have been published on MEGxp0_000012.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072208112D          

 38 42  0  0  1  0            999 V2000
    5.3194    0.6825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7674    0.0694    0.0000 C   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


  Mrv1652309072208112D          

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 15 16  1  1  0  0  0
  4 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 19 24  1  0  0  0  0
  3 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 26 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 37 38  1  0  0  0  0
 33 38  2  0  0  0  0
 30 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0245199

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=COC(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(C=C)C1CC1=NC=CC2=C1NC1=C2C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H30N2O9/c1-3-13-16(10-19-21-15(8-9-28-19)14-6-4-5-7-18(14)29-21)17(25(34)35-2)12-36-26(13)38-27-24(33)23(32)22(31)20(11-30)37-27/h3-9,12-13,16,20,22-24,26-27,29-33H,1,10-11H2,2H3/t13?,16?,20-,22-,23+,24-,26?,27+/m1/s1

> <INCHI_KEY>
VXUXCAXVQWIEMN-AXAZIGGNSA-N

> <FORMULA>
C27H30N2O9

> <MOLECULAR_WEIGHT>
526.542

> <EXACT_MASS>
526.195130554

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
53.852429478557674

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 3-ethenyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylate

> <JCHEM_LOGP>
0.6965941983333337

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.071744818121985

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.189945969778742

> <JCHEM_PKA_STRONGEST_BASIC>
5.662121707993897

> <JCHEM_POLAR_SURFACE_AREA>
163.59

> <JCHEM_REFRACTIVITY>
132.70909999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
methyl 5-ethenyl-4-{9H-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4H-pyran-3-carboxylate

> <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       9.930   1.274   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.899   0.130   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.375  -1.335   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.881  -1.655   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      11.912  -0.511   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      13.418  -0.831   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      14.449   0.314   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      15.955  -0.007   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      16.985   1.138   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      18.492   0.818   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      16.431  -1.471   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      17.937  -1.791   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      15.400  -2.616   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      15.876  -4.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      13.894  -2.296   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.864  -3.440   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      11.357  -3.120   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.327  -4.264   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.820  -3.944   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.790  -5.089   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.284  -4.768   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       8.266  -6.553   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       7.235  -7.698   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.344  -2.479   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.838  -2.159   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0       7.393   0.450   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.173   0.450   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   24                                                  
CONECT    4    3    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    6   16                                                  
CONECT   16   15                                                            
CONECT   17    4   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22                                                            
CONECT   24   19    3   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   31                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   38                                                  
CONECT   31   30   26   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   33   30                                                  
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₀N₂O₉

Average Mass

526.5420 Da

Monoisotopic Mass

526.19513 Da

IUPAC Name

methyl 3-ethenyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylate

Traditional Name

methyl 5-ethenyl-4-{9H-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4H-pyran-3-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=COC(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(C=C)C1CC1=NC=CC2=C1NC1=C2C=CC=C1

InChI Identifier

InChI=1S/C27H30N2O9/c1-3-13-16(10-19-21-15(8-9-28-19)14-6-4-5-7-18(14)29-21)17(25(34)35-2)12-36-26(13)38-27-24(33)23(32)22(31)20(11-30)37-27/h3-9,12-13,16,20,22-24,26-27,29-33H,1,10-11H2,2H3/t13?,16?,20-,22-,23+,24-,26?,27+/m1/s1

InChI Key

VXUXCAXVQWIEMN-AXAZIGGNSA-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
Chimarrhis turbinata	LOTUS Database	35616633
Ochrosia moorei	LOTUS Database	35616633
Strychnos mellodora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Harman
Beta-carboline
Pyridoindole
Glycosyl compound
Secoiridoid-skeleton
O-glycosyl compound
Aromatic monoterpenoid
Monoterpenoid
Indole
Indole or derivatives
Alkaloid or derivatives
Sugar acid
Monosaccharide
Oxane
Pyridine
Benzenoid
Pyrrole
Vinylogous ester
Enoate ester
Methyl ester
Alpha,beta-unsaturated carboxylic ester
Heteroaromatic compound
Secondary alcohol
Carboxylic acid ester
Polyol
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Acetal
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Alcohol
Organooxygen compound
Organic nitrogen compound
Organic oxygen compound
Carbonyl group
Primary alcohol
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	0.7	ChemAxon
pKa (Strongest Acidic)	12.19	ChemAxon
pKa (Strongest Basic)	5.66	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	163.59 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	132.71 m³·mol⁻¹	ChemAxon
Polarizability	53.85 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	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

4475623

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5316604

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate (NP0245199)

MOL for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

3D MOL for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

3D SDF for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

3D-SDF for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

PDB for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

3D PDB for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

SMILES for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

INCHI for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

Structure for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)

3D Structure for NP0245199 (methyl 5-ethenyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylate)