NP-MRD: Showing NP-Card for (-)-Naucleofficine C (NP0073631)

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Record Information

Version

2.0

Created at

2022-04-28 18:51:40 UTC

Updated at

2022-04-28 18:51:40 UTC

NP-MRD ID

NP0073631

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Naucleofficine C

Description

4-[(2E)-1-hydroxybut-2-en-2-yl]-15-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,17-diazatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]Heptadeca-1(10),2,4,11(16),12,14-hexaen-6-one 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. (-)-Naucleofficine C is found in Nauclea officinalis . Based on a literature review very few articles have been published on 4-[(2E)-1-hydroxybut-2-en-2-yl]-15-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,17-diazatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]Heptadeca-1(10),2,4,11(16),12,14-hexaen-6-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282220512D          

 35 39  0  0  1  0            999 V2000
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M  END

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M  END


  Mrv1652304282220512D          

 35 39  0  0  1  0            999 V2000
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    5.1552    2.4387    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0073631

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C(\CO)C1=CC(=O)N2CCC3=C(NC4=C(O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)C=CC=C34)C2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H28N2O8/c1-2-12(10-28)13-8-16-20-15(6-7-27(16)19(30)9-13)14-4-3-5-17(21(14)26-20)34-25-24(33)23(32)22(31)18(11-29)35-25/h2-5,8-9,18,22-26,28-29,31-33H,6-7,10-11H2,1H3/b12-2-/t18-,22-,23+,24-,25-/m1/s1

> <INCHI_KEY>
DAFXFTIFCFNTII-RMKZHMHMSA-N

> <FORMULA>
C25H28N2O8

> <MOLECULAR_WEIGHT>
484.505

> <EXACT_MASS>
484.18456587

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
49.98779794304939

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(2E)-1-hydroxybut-2-en-2-yl]-15-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,17-diazatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,11,13,15-hexaen-6-one

> <ALOGPS_LOGP>
1.20

> <JCHEM_LOGP>
-1.2413722256666653

> <ALOGPS_LOGS>
-2.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.740016441785777

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.095666571663623

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7547976136596186

> <JCHEM_POLAR_SURFACE_AREA>
155.71

> <JCHEM_REFRACTIVITY>
127.68129999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.21e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[(2E)-1-hydroxybut-2-en-2-yl]-15-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,17-diazatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,11,13,15-hexaen-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  O   UNK     0       8.254   3.847   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       9.623   4.552   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.696   6.091   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.065   6.796   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.361   5.964   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.287   4.426   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      10.919   3.720   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      13.583   3.593   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      14.952   4.299   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      13.729   6.670   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      11.138   8.335   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       8.401   6.923   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.181   2.308   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.812   1.603   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.739   0.064   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.035  -0.768   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.404  -0.063   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.477   1.476   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.254  -0.341   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.409   0.946   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       5.372   2.147   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       2.871   0.858   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       2.179  -0.517   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       3.024  -1.805   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.561  -1.717   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.641  -0.606   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.051  -1.981   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -0.204   0.682   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.489   2.057   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.026   2.146   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.356   3.345   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.894   3.257   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.586   1.881   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.336   4.720   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -0.509   6.008   0.000  0.00  0.00           O+0
CONECT    1    2   13                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4   12                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9                                                       
CONECT    9    8                                                            
CONECT   10    5                                                            
CONECT   11    4                                                            
CONECT   12    3                                                            
CONECT   13    1   14   18                                                  
CONECT   14   13   15   21                                                  
CONECT   15   14   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   13                                                       
CONECT   19   15   20   25                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20   14                                                       
CONECT   22   20   23   30                                                  
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24   19                                                       
CONECT   26   23   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29   22                                                       
CONECT   31   29   32   34                                                  
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   31   35                                                       
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₈N₂O₈

Average Mass

484.5050 Da

Monoisotopic Mass

484.18457 Da

IUPAC Name

4-[(2E)-1-hydroxybut-2-en-2-yl]-15-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,17-diazatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,11,13,15-hexaen-6-one

Traditional Name

4-[(2E)-1-hydroxybut-2-en-2-yl]-15-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,17-diazatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,11,13,15-hexaen-6-one

CAS Registry Number

Not Available

SMILES

C\C=C(\CO)C1=CC(=O)N2CCC3=C(NC4=C(O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)C=CC=C34)C2=C1

InChI Identifier

InChI=1S/C25H28N2O8/c1-2-12(10-28)13-8-16-20-15(6-7-27(16)19(30)9-13)14-4-3-5-17(21(14)26-20)34-25-24(33)23(32)22(31)18(11-29)35-25/h2-5,8-9,18,22-26,28-29,31-33H,6-7,10-11H2,1H3/b12-2-/t18-,22-,23+,24-,25-/m1/s1

InChI Key

DAFXFTIFCFNTII-RMKZHMHMSA-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 officinalis	Plant	KNApSAcK

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
3-alkylindole
Quinolizine
Indole
Indole or derivatives
Pyridinone
Monosaccharide
Oxane
Benzenoid
Pyridine
Heteroaromatic compound
Pyrrole
Lactam
Secondary alcohol
Polyol
Organoheterocyclic compound
Azacycle
Oxacycle
Acetal
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Primary alcohol
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	1.2	ALOGPS
logP	-1.2	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	12.1	ChemAxon
pKa (Strongest Basic)	-1.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	155.71 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	127.68 m³·mol⁻¹	ChemAxon
Polarizability	49.99 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	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

24862705

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Naucleofficine C (NP0073631)

MOL for NP0073631 ((-)-Naucleofficine C)

3D MOL for NP0073631 ((-)-Naucleofficine C)

3D SDF for NP0073631 ((-)-Naucleofficine C)

3D-SDF for NP0073631 ((-)-Naucleofficine C)

PDB for NP0073631 ((-)-Naucleofficine C)

3D PDB for NP0073631 ((-)-Naucleofficine C)

SMILES for NP0073631 ((-)-Naucleofficine C)

INCHI for NP0073631 ((-)-Naucleofficine C)

Structure for NP0073631 ((-)-Naucleofficine C)

3D Structure for NP0073631 ((-)-Naucleofficine C)