NP-MRD: Showing NP-Card for (1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol (NP0179241)

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Record Information

Version

2.0

Created at

2022-09-03 17:23:50 UTC

Updated at

2022-09-03 17:23:50 UTC

NP-MRD ID

NP0179241

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol

Description

(1S)-1-{13,15-dioxa-8-azatetracyclo[8.7.0.0²,⁷.0¹²,¹⁶]Heptadeca-1(17),2(7),3,5,8,10,12(16)-heptaen-6-yl}ethane-1,2-diol 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. (1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol is found in Crinum asiaticum. Based on a literature review very few articles have been published on (1S)-1-{13,15-dioxa-8-azatetracyclo[8.7.0.0²,⁷.0¹²,¹⁶]Heptadeca-1(17),2(7),3,5,8,10,12(16)-heptaen-6-yl}ethane-1,2-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 37  0  0  0  0  0  0  0  0999 V2000
   -4.7979    0.2808    1.6189 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7152   -0.1433    0.3051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4053   -0.7877   -0.0471 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4655   -1.1774   -1.3886 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2870    0.1593    0.1076 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4925    1.4757    0.4031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4196    2.3651    0.5426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1266    1.9233    0.3826 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0913    0.5966    0.0841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9711   -0.2903   -0.0553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7622   -1.5857   -0.3467 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4754   -2.0673   -0.5128 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5935   -1.2431   -0.3895 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8677   -1.7497   -0.5630 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9684   -0.9440   -0.4432 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7785    0.3798   -0.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4814    0.8893    0.0286 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3649    0.0959   -0.0878 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0247    0.9907   -0.0763 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0371    0.0002   -0.0574 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3496   -1.1364   -0.5539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7287    0.2904    1.9555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9582    0.7347   -0.3471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5564   -0.8650    0.0802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2651   -1.6453    0.6274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9396   -0.4966   -1.9271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4995    1.8388    0.5286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6881    3.3852    0.7771 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6643    2.6328    0.4970 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6852   -3.1168   -0.7511 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0225   -2.7914   -0.7967 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3602    1.9277    0.2596 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4175   -0.1859    0.9856 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8964    0.2599   -0.6934 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 16 17  1  0
 17 18  2  0
 18  9  1  0
  9  8  2  0
  8  7  1  0
  7  6  2  0
  6  5  1  0
  9 10  1  0
 18 13  1  0
 21 15  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  1
  4 26  1  0
 12 30  1  0
 14 31  1  0
 20 33  1  0
 20 34  1  0
 17 32  1  0
  8 29  1  0
  7 28  1  0
  6 27  1  0
M  END


  Mrv1652309032219232D          

 21 24  0  0  1  0            999 V2000
    0.4503    0.9219    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9821    0.2912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7942    0.4364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0745    1.2123    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3261   -0.1943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0458   -0.9702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5776   -1.6009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3897   -1.4557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6700   -0.6798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1382   -0.0491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4185    0.7268    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2306    0.8721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7624    0.2414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5745    0.3866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1064   -0.2441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8261   -1.0201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0139   -1.1653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4821   -0.5346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4774   -1.5264    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1602   -1.0634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9309   -0.2709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  5 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
  9 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 15 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0179241

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H](O)C1=C2N=CC3=CC4=C(OCO4)C=C3C2=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C16H13NO4/c18-7-13(19)11-3-1-2-10-12-5-15-14(20-8-21-15)4-9(12)6-17-16(10)11/h1-6,13,18-19H,7-8H2/t13-/m1/s1

> <INCHI_KEY>
YMXGETAKQNEFRX-CYBMUJFWSA-N

> <FORMULA>
C16H13NO4

> <MOLECULAR_WEIGHT>
283.283

> <EXACT_MASS>
283.084457903

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
29.46114361281949

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S)-1-{13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),2,4,6,8,10,12(16)-heptaen-6-yl}ethane-1,2-diol

> <JCHEM_LOGP>
1.3459259863333335

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.503872417891422

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.63869812396857

> <JCHEM_PKA_STRONGEST_BASIC>
4.405912187024169

> <JCHEM_POLAR_SURFACE_AREA>
71.81

> <JCHEM_REFRACTIVITY>
74.97480000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S)-1-{13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),2,4,6,8,10,12(16)-heptaen-6-yl}ethane-1,2-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  O   UNK     0       0.841   1.721   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.833   0.544   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.349   0.815   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.872   2.263   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.342  -0.363   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.819  -1.811   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.811  -2.988   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.327  -2.717   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.851  -1.269   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.858  -0.092   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       6.381   1.357   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       7.897   1.628   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.890   0.451   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.406   0.722   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.399  -0.456   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.875  -1.904   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.359  -2.175   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.367  -0.998   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      12.091  -2.849   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      13.366  -1.985   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      12.938  -0.506   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   18                                                  
CONECT   10    9    5   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   21                                                  
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17   13    9                                                  
CONECT   19   16   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   15                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₃NO₄

Average Mass

283.2830 Da

Monoisotopic Mass

283.08446 Da

IUPAC Name

(1S)-1-{13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),2,4,6,8,10,12(16)-heptaen-6-yl}ethane-1,2-diol

Traditional Name

(1S)-1-{13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),2,4,6,8,10,12(16)-heptaen-6-yl}ethane-1,2-diol

CAS Registry Number

Not Available

SMILES

OC[C@@H](O)C1=C2N=CC3=CC4=C(OCO4)C=C3C2=CC=C1

InChI Identifier

InChI=1S/C16H13NO4/c18-7-13(19)11-3-1-2-10-12-5-15-14(20-8-21-15)4-9(12)6-17-16(10)11/h1-6,13,18-19H,7-8H2/t13-/m1/s1

InChI Key

YMXGETAKQNEFRX-CYBMUJFWSA-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
Crinum asiaticum	LOTUS Database	35616633

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
Isoquinoline
Benzodioxole
Pyridine
Benzenoid
Heteroaromatic compound
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Acetal
Aromatic alcohol
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
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	1.35	ChemAxon
pKa (Strongest Acidic)	13.64	ChemAxon
pKa (Strongest Basic)	4.41	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	71.81 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	74.97 m³·mol⁻¹	ChemAxon
Polarizability	29.46 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

162893675

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol (NP0179241)

MOL for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

3D MOL for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

3D SDF for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

3D-SDF for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

PDB for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

3D PDB for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

SMILES for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

INCHI for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

Structure for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)

3D Structure for NP0179241 ((1s)-1-{9h-[1,3]dioxolo[4,5-j]phenanthridin-4-yl}ethane-1,2-diol)