NP-MRD: Showing NP-Card for methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate (NP0301109)

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Record Information

Version

2.0

Created at

2022-09-10 13:52:02 UTC

Updated at

2022-09-10 13:52:02 UTC

NP-MRD ID

NP0301109

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate

Description

Methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9H-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate 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. methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate is found in Stellaria dichotoma. Methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9H-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004241502582D          

 37 40  0  0  0  0            999 V2000
    3.6003    0.7238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7933    0.5522    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.7314   -0.4039    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


  Mrv1533004241502582D          

 37 40  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0301109

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C=CNC(=O)C1=CC2=C(NC3=C2C=CC=C3OC2OC(CO)C(O)C(O)C2O)C(=N1)C(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H25N3O10/c1-10(29)17-19-12(8-13(26-17)23(34)25-7-6-16(30)35-2)11-4-3-5-14(18(11)27-19)36-24-22(33)21(32)20(31)15(9-28)37-24/h3-8,15,20-22,24,27-28,31-33H,9H2,1-2H3,(H,25,34)

> <INCHI_KEY>
UMGPWCXTJXKPHK-UHFFFAOYSA-N

> <FORMULA>
C24H25N3O10

> <MOLECULAR_WEIGHT>
515.475

> <EXACT_MASS>
515.153994017

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
51.62816929491166

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9H-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate

> <ALOGPS_LOGP>
0.31

> <JCHEM_LOGP>
-0.9847154573333334

> <ALOGPS_LOGS>
-2.93

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.200387660475846

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.0185476863084

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3284924195440654

> <JCHEM_POLAR_SURFACE_AREA>
200.52999999999997

> <JCHEM_REFRACTIVITY>
124.85140000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.02e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9H-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       6.721   1.351   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       5.214   1.031   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.738  -0.434   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.769  -1.578   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.232  -0.754   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.202   0.390   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.695   0.070   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.219  -1.394   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.287  -1.715   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.250  -2.539   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.756  -2.219   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.787  -3.363   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.327  -3.363   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.357  -2.219   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.863  -2.539   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.339  -4.003   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.309  -5.148   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       7.785  -6.612   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       9.291  -6.933   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      10.322  -5.788   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      11.828  -6.108   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.858  -4.964   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      12.382  -3.499   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      12.304  -7.573   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      13.810  -7.893   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      11.273  -8.717   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      11.749 -10.182   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       9.767  -8.397   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       8.736  -9.542   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       5.802  -4.828   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0       4.557  -5.733   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       3.311  -4.828   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.804  -5.148   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0       0.774  -4.003   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       1.328  -6.612   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -0.178  -6.933   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       2.359  -7.757   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   34                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   32                                                  
CONECT   13   12   14   30                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   28                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   24                                                  
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   21   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   19   29                                                  
CONECT   29   28                                                            
CONECT   30   17   13   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   12   33                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33   10                                                       
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Value	Source
Methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9H-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoic acid	Generator

Chemical Formula

C₂₄H₂₅N₃O₁₀

Average Mass

515.4750 Da

Monoisotopic Mass

515.15399 Da

IUPAC Name

methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9H-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate

Traditional Name

methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9H-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate

CAS Registry Number

Not Available

SMILES

COC(=O)C=CNC(=O)C1=CC2=C(NC3=C2C=CC=C3OC2OC(CO)C(O)C(O)C2O)C(=N1)C(C)=O

InChI Identifier

InChI=1S/C24H25N3O10/c1-10(29)17-19-12(8-13(26-17)23(34)25-7-6-16(30)35-2)11-4-3-5-14(18(11)27-19)36-24-22(33)21(32)20(31)15(9-28)37-24/h3-8,15,20-22,24,27-28,31-33H,9H2,1-2H3,(H,25,34)

InChI Key

UMGPWCXTJXKPHK-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
Stellaria dichotoma	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
Harman
Beta-carboline
Pyridoindole
Hexose monosaccharide
O-glycosyl compound
Indole
Indole or derivatives
Pyridine carboxylic acid or derivatives
Alkaloid or derivatives
2-heteroaryl carboxamide
Aryl alkyl ketone
Aryl ketone
Monosaccharide
Oxane
Benzenoid
Pyridine
Heteroaromatic compound
Acrylic acid or derivatives
Vinylogous amide
Alpha,beta-unsaturated carboxylic ester
Pyrrole
Methyl ester
Enoate ester
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Ketone
Carboxylic acid ester
Polyol
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Aldehyde
Organic nitrogen compound
Organopnictogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organonitrogen compound
Primary alcohol
Carbonyl group
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	0.31	ALOGPS
logP	-0.98	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	10.02	ChemAxon
pKa (Strongest Basic)	-0.33	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	200.53 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	124.85 m³·mol⁻¹	ChemAxon
Polarizability	51.63 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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate (NP0301109)

MOL for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

3D MOL for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

3D SDF for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

3D-SDF for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

PDB for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

3D PDB for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

SMILES for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

INCHI for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

Structure for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)

3D Structure for NP0301109 (methyl 3-[(1-acetyl-8-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9h-pyrido[3,4-b]indol-3-yl)formamido]prop-2-enoate)