NP-MRD: Showing NP-Card for (-)-Naucleoside A (NP0080761)

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Record Information

Version

2.0

Created at

2022-04-29 01:45:13 UTC

Updated at

2022-04-29 01:45:13 UTC

NP-MRD ID

NP0080761

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Naucleoside A

Description

(18R,19S,20S)-19-ethenyl-16-hydroxy-18-{[(2S,3R,4S,5R,6R)-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-hexaen-14-one belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety. (-)-Naucleoside A is found in Nauclea orientalis . Based on a literature review very few articles have been published on (18R,19S,20S)-19-ethenyl-16-hydroxy-18-{[(2S,3R,4S,5R,6R)-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-hexaen-14-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292203452D          

 37 42  0  0  1  0            999 V2000
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 36 37  1  0  0  0  0
  7 37  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292203452D          

 37 42  0  0  1  0            999 V2000
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 28 29  1  0  0  0  0
 25 30  1  1  0  0  0
 24 31  1  1  0  0  0
 14 32  1  0  0  0  0
 13 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 10 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
  7 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0080761

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2OC(O)=C3[C@@H](C=C4N(CCC5=C4NC4=CC=CC=C54)C3=O)[C@@H]2C=C)[C@H](O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28N2O9/c1-2-11-14-9-16-19-13(12-5-3-4-6-15(12)27-19)7-8-28(16)23(33)18(14)24(34)36-25(11)37-26-22(32)21(31)20(30)17(10-29)35-26/h2-6,9,11,14,17,20-22,25-27,29-32,34H,1,7-8,10H2/t11-,14-,17+,20-,21-,22+,25-,26-/m0/s1

> <INCHI_KEY>
QJMQBJILYFAVTF-LAQQPVFWSA-N

> <FORMULA>
C26H28N2O9

> <MOLECULAR_WEIGHT>
512.515

> <EXACT_MASS>
512.17948049

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
53.010160896282414

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(18R,19S,20S)-19-ethenyl-16-hydroxy-18-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,10}.0^{4,9}.0^{15,20}]henicosa-1(21),2(10),4,6,8,15-hexaen-14-one

> <ALOGPS_LOGP>
0.70

> <JCHEM_LOGP>
-0.07929582733333235

> <ALOGPS_LOGS>
-2.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.20800010751195

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.033245657641038

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810847616078684

> <JCHEM_POLAR_SURFACE_AREA>
164.94000000000003

> <JCHEM_REFRACTIVITY>
139.62279999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.63e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(18R,19S,20S)-19-ethenyl-16-hydroxy-18-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,10}.0^{4,9}.0^{15,20}]henicosa-1(21),2(10),4,6,8,15-hexaen-14-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0      11.961   0.113   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.834   1.648   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.441   2.305   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.176   1.427   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.303  -0.108   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.696  -0.765   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.883  -0.703   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.878   0.464   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       7.677   1.780   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       5.365   0.177   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.360   1.344   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.847   1.057   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.339  -0.397   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.826  -0.684   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.179   0.483   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.329   1.937   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.842   2.224   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.350   3.678   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.863   3.965   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.676   3.104   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -2.189   2.817   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.697   1.363   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.692   0.196   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -4.210   1.076   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -5.215   2.243   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.707   3.697   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -3.194   3.984   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -5.712   4.863   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -7.226   4.577   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -6.728   1.956   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -4.718  -0.378   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       0.318  -2.138   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.344  -1.564   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       2.836  -3.017   0.000  0.00  0.00           O+0
HETATM   35  N   UNK     0       4.857  -1.277   0.000  0.00  0.00           N+0
HETATM   36  C   UNK     0       5.862  -2.444   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       7.375  -2.157   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   37                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8   11   35                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   33                                                  
CONECT   14   13   15   32                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   12   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   16   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   31                                                  
CONECT   25   24   26   30                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26   21                                                       
CONECT   28   26   29                                                       
CONECT   29   28                                                            
CONECT   30   25                                                            
CONECT   31   24                                                            
CONECT   32   14                                                            
CONECT   33   13   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   10   36                                                  
CONECT   36   35   37                                                       
CONECT   37   36    7                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈N₂O₉

Average Mass

512.5150 Da

Monoisotopic Mass

512.17948 Da

IUPAC Name

(18R,19S,20S)-19-ethenyl-16-hydroxy-18-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,10}.0^{4,9}.0^{15,20}]henicosa-1(21),2(10),4,6,8,15-hexaen-14-one

Traditional Name

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2OC(O)=C3[C@@H](C=C4N(CCC5=C4NC4=CC=CC=C54)C3=O)[C@@H]2C=C)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C26H28N2O9/c1-2-11-14-9-16-19-13(12-5-3-4-6-15(12)27-19)7-8-28(16)23(33)18(14)24(34)36-25(11)37-26-22(32)21(31)20(30)17(10-29)35-26/h2-6,9,11,14,17,20-22,25-27,29-32,34H,1,7-8,10H2/t11-,14-,17+,20-,21-,22+,25-,26-/m0/s1

InChI Key

QJMQBJILYFAVTF-LAQQPVFWSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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 orientalis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyridoindoles

Direct Parent

Beta carbolines

Alternative Parents

Substituents

Beta-carboline
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
3-alkylindole
Indole
Tetrahydropyridine
Benzenoid
Oxane
Monosaccharide
Heteroaromatic compound
Vinylogous ester
Vinylogous acid
Tertiary carboxylic acid amide
Pyrrole
Secondary alcohol
Lactam
Ketene acetal or derivatives
Carboxamide group
Oxacycle
Azacycle
Polyol
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
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	ALOGPS
logP	-0.079	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	10.03	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	164.94 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	139.62 m³·mol⁻¹	ChemAxon
Polarizability	53.01 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	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

162949796

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for (-)-Naucleoside A (NP0080761)

MOL for NP0080761 ((-)-Naucleoside A)

3D MOL for NP0080761 ((-)-Naucleoside A)

3D SDF for NP0080761 ((-)-Naucleoside A)

3D-SDF for NP0080761 ((-)-Naucleoside A)

PDB for NP0080761 ((-)-Naucleoside A)

3D PDB for NP0080761 ((-)-Naucleoside A)

SMILES for NP0080761 ((-)-Naucleoside A)

INCHI for NP0080761 ((-)-Naucleoside A)

Structure for NP0080761 ((-)-Naucleoside A)

3D Structure for NP0080761 ((-)-Naucleoside A)