NP-MRD: Showing NP-Card for 19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione (NP0257939)

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Record Information

Version

2.0

Created at

2022-09-07 23:12:39 UTC

Updated at

2022-09-07 23:12:39 UTC

NP-MRD ID

NP0257939

Secondary Accession Numbers

None

Natural Product Identification

Common Name

19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione

Description

19-Ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]Henicosa-1(21),2(10),4(9),5,7,15(20)-hexaene-14,16-dione 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. 19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione is found in Nauclea officinalis. 19-Ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]Henicosa-1(21),2(10),4(9),5,7,15(20)-hexaene-14,16-dione is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251509082D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004251509082D          

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 16 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  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 21 30  1  0  0  0  0
 30 31  1  0  0  0  0
 19 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 15 35  1  0  0  0  0
 18 35  1  0  0  0  0
 12 36  1  0  0  0  0
  8 36  1  0  0  0  0
 36 37  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0257939

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC=C1COC(=O)C2=C1C=C1N(CCC3=C1NC1=C(OC4OC(CO)C(O)C(O)C4O)C=CC=C31)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H26N2O9/c1-2-11-10-35-25(34)18-14(11)8-15-19-13(6-7-28(15)24(18)33)12-4-3-5-16(20(12)27-19)36-26-23(32)22(31)21(30)17(9-29)37-26/h2-5,8,17,21-23,26-27,29-32H,6-7,9-10H2,1H3

> <INCHI_KEY>
XDZBDGFFSCAVBI-UHFFFAOYSA-N

> <FORMULA>
C26H26N2O9

> <MOLECULAR_WEIGHT>
510.499

> <EXACT_MASS>
510.163830425

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
51.64643470940342

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione

> <ALOGPS_LOGP>
1.32

> <JCHEM_LOGP>
-0.7563246793333321

> <ALOGPS_LOGS>
-2.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.737256450896119

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.094507804388515

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923518440404

> <JCHEM_POLAR_SURFACE_AREA>
161.78

> <JCHEM_REFRACTIVITY>
130.26340000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.21e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0      10.558  -3.304   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.553  -2.138   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.061  -0.684   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.574  -0.397   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      12.082   1.057   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      11.077   2.224   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.585   3.678   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.564   1.937   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.056   0.483   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.543   0.196   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.538   1.363   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       7.046   2.817   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       6.041   3.984   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.527   3.697   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.019   2.243   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.025   1.076   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       4.225  -0.240   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       2.726   0.113   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.461  -0.765   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.588  -2.299   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.323  -3.177   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.450  -4.712   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.816  -5.589   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.688  -7.124   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.704  -7.781   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -2.208  -4.932   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -3.474  -5.810   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.336  -3.397   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -3.728  -2.740   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -1.070  -2.520   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.197  -0.985   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       0.068  -0.108   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.059   1.427   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.206   2.305   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.599   1.648   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       8.559   3.104   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       9.067   4.557   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   36                                                  
CONECT    9    8    3   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   36                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   35                                                  
CONECT   16   15   11   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   35                                                  
CONECT   19   18   20   32                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   30                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   21   31                                                  
CONECT   31   30                                                            
CONECT   32   19   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   15   18                                                  
CONECT   36   12    8   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₆N₂O₉

Average Mass

510.4990 Da

Monoisotopic Mass

510.16383 Da

IUPAC Name

19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione

Traditional Name

19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione

CAS Registry Number

Not Available

SMILES

CC=C1COC(=O)C2=C1C=C1N(CCC3=C1NC1=C(OC4OC(CO)C(O)C(O)C4O)C=CC=C31)C2=O

InChI Identifier

InChI=1S/C26H26N2O9/c1-2-11-10-35-25(34)18-14(11)8-15-19-13(6-7-28(15)24(18)33)12-4-3-5-16(20(12)27-19)36-26-23(32)22(31)21(30)17(9-29)37-26/h2-5,8,17,21-23,26-27,29-32H,6-7,9-10H2,1H3

InChI Key

XDZBDGFFSCAVBI-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
Nauclea officinalis	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
Beta-carboline
Pyridoindole
Hexose monosaccharide
O-glycosyl compound
Pyranopyridine
3-alkylindole
Indole
Indole or derivatives
Pyridine carboxylic acid
Pyridinone
Monosaccharide
Oxane
Benzenoid
Pyridine
Heteroaromatic compound
Vinylogous amide
Pyrrole
Secondary alcohol
Carboxylic acid ester
Lactam
Lactone
Organoheterocyclic compound
Carboxylic acid derivative
Polyol
Azacycle
Monocarboxylic acid or derivatives
Acetal
Oxacycle
Organic oxide
Hydrocarbon derivative
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	1.32	ALOGPS
logP	-0.76	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	12.09	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	161.78 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	130.26 m³·mol⁻¹	ChemAxon
Polarizability	51.65 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

74337036

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione (NP0257939)

MOL for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

3D MOL for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

3D SDF for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

3D-SDF for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

PDB for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

3D PDB for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

SMILES for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

INCHI for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

Structure for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)

3D Structure for NP0257939 (19-ethylidene-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2(10),4,6,8,15(20)-hexaene-14,16-dione)