NP-MRD: Showing NP-Card for (1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol (NP0239749)

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Record Information

Version

2.0

Created at

2022-09-06 23:24:21 UTC

Updated at

2022-09-06 23:24:21 UTC

NP-MRD ID

NP0239749

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol

Description

(2R,3R,4S,5S,6S,7R)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-13,15-dioxa-8-azatetracyclo[8.7.0.0²,⁷.0¹²,¹⁶]Heptadeca-1(17),8,10,12(16)-tetraene-3,5,6,9,11-pentol belongs to the class of organic compounds known as phenanthridines and derivatives. These are polycyclic compounds containing a phenanthridine moiety, which is a tricyclic system with two benzene rings joined by a pyridine forming a non-linear skeleton. Hydrogenated derivatives are also included. Based on a literature review very few articles have been published on (2R,3R,4S,5S,6S,7R)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-13,15-dioxa-8-azatetracyclo[8.7.0.0²,⁷.0¹²,¹⁶]Heptadeca-1(17),8,10,12(16)-tetraene-3,5,6,9,11-pentol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072201242D          

 34 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072201242D          

 34 38  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0239749

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@@H](O)[C@@H]3N=C(O)C4=C(C=C5OCOC5=C4O)[C@H]3[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H25NO13/c22-2-6-10(23)14(27)16(29)20(33-6)34-18-11(24)7-4-1-5-17(32-3-31-5)12(25)8(4)19(30)21-9(7)13(26)15(18)28/h1,6-7,9-11,13-16,18,20,22-29H,2-3H2,(H,21,30)/t6-,7-,9-,10-,11-,13+,14+,15+,16-,18+,20+/m1/s1

> <INCHI_KEY>
QSYBPQCJMIBVOY-YYEKDKEWSA-N

> <FORMULA>
C20H25NO13

> <MOLECULAR_WEIGHT>
487.414

> <EXACT_MASS>
487.132589869

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
46.089981339344945

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6S,7R)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),8,11,16-tetraene-3,5,6,9,11-pentol

> <JCHEM_LOGP>
-2.8672573830000005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.856668377506294

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.942901345200623

> <JCHEM_PKA_STRONGEST_BASIC>
2.06657829272915

> <JCHEM_POLAR_SURFACE_AREA>
231.34999999999994

> <JCHEM_REFRACTIVITY>
105.58590000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6S,7R)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),8,11,16-tetraene-3,5,6,9,11-pentol

> <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  O   UNK     0     -10.247  -0.185   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -8.731  -0.456   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -7.738   0.722   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -6.222   0.451   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -5.230   1.628   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.714   1.357   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.191  -0.092   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.183  -1.269   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -5.699  -0.998   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -3.660  -2.717   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -4.653  -3.895   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.144  -2.988   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -1.621  -4.437   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -0.105  -4.708   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.418  -6.156   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.888  -3.531   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.365  -2.082   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.357  -0.905   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.873  -1.176   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.396  -2.624   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.404  -3.802   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.927  -5.250   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       4.936  -2.574   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       5.364  -1.095   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       4.089  -0.231   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -1.151  -1.811   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.675  -0.363   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -0.682   0.815   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -5.753   3.076   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -4.760   4.254   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -7.269   3.347   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -7.792   4.796   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -8.262   2.170   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -9.778   2.441   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   33                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   29                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   27                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   26                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   21                                                  
CONECT   17   16   18   26                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   25                                                  
CONECT   20   19   21   23                                                  
CONECT   21   20   16   22                                                  
CONECT   22   21                                                            
CONECT   23   20   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   19                                                       
CONECT   26   17   12   27                                                  
CONECT   27   26    7   28                                                  
CONECT   28   27                                                            
CONECT   29    5   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31    3   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₅NO₁₃

Average Mass

487.4140 Da

Monoisotopic Mass

487.13259 Da

IUPAC Name

(2R,3R,4S,5S,6S,7R)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),8,11,16-tetraene-3,5,6,9,11-pentol

Traditional Name

(2R,3R,4S,5S,6S,7R)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),8,11,16-tetraene-3,5,6,9,11-pentol

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@@H](O)[C@@H]3N=C(O)C4=C(C=C5OCOC5=C4O)[C@H]3[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C20H25NO13/c22-2-6-10(23)14(27)16(29)20(33-6)34-18-11(24)7-4-1-5-17(32-3-31-5)12(25)8(4)19(30)21-9(7)13(26)15(18)28/h1,6-7,9-11,13-16,18,20,22-29H,2-3H2,(H,21,30)/t6-,7-,9-,10-,11-,13+,14+,15+,16-,18+,20+/m1/s1

InChI Key

QSYBPQCJMIBVOY-YYEKDKEWSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthridines and derivatives. These are polycyclic compounds containing a phenanthridine moiety, which is a tricyclic system with two benzene rings joined by a pyridine forming a non-linear skeleton. Hydrogenated derivatives are also included.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolines and derivatives

Sub Class

Benzoquinolines

Direct Parent

Phenanthridines and derivatives

Alternative Parents

Substituents

Phenanthridine
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Dihydroisoquinoline
Benzodioxole
1-hydroxy-4-unsubstituted benzenoid
Cyclitol or derivatives
Monosaccharide
Oxane
Benzenoid
Cyclic carboximidic acid
Cyclic alcohol
Secondary alcohol
Polyol
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Oxacycle
Acetal
Primary alcohol
Organic nitrogen compound
Organopnictogen compound
Alcohol
Organonitrogen compound
Hydrocarbon derivative
Organooxygen compound
Organic oxygen 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	-2.9	ChemAxon
pKa (Strongest Acidic)	6.94	ChemAxon
pKa (Strongest Basic)	2.07	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	231.35 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	105.59 m³·mol⁻¹	ChemAxon
Polarizability	46.09 Å³	ChemAxon
Number of Rings	5	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

163022604

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol (NP0239749)

MOL for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

3D MOL for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

3D SDF for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

3D-SDF for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

PDB for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

3D PDB for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

SMILES for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

INCHI for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

Structure for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)

3D Structure for NP0239749 ((1r,2s,3s,4s,4ar,11br)-2-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,2h,3h,4h,4ah,9h,11bh-[1,3]dioxolo[4,5-j]phenanthridine-1,3,4,6,7-pentol)