NP-MRD: Showing NP-Card for (2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol (NP0224102)

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Record Information

Version

2.0

Created at

2022-09-06 02:23:06 UTC

Updated at

2022-09-06 02:23:07 UTC

NP-MRD ID

NP0224102

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol

Description

(4R,5R,6S,7R)-13,15-dioxa-8-azatetracyclo[8.7.0.0²,⁷.0¹²,¹⁶]Heptadeca-1(17),2,8,10,12(16)-pentaene-4,5,6,9,11-pentol belongs to the class of organic compounds known as phenanthridine- and phenanthridone-type amaryllidaceae alkaloids. These are amaryllidaceae alkaloids compounds based on the phenanthridine or the phenanthridone skeleton. Phenanthridone-type alkaloids have the highest oxygenated C ring in all Amaryllidaceae alkaloids, and they always show an amide group in ring B. On the contrary, alkaloids of the phenanthridine type often show completely aromatic ring system, occasionally with a methylation quaternary nitrogen atom. (2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol is found in Lycoris radiata. Based on a literature review very few articles have been published on (4R,5R,6S,7R)-13,15-dioxa-8-azatetracyclo[8.7.0.0²,⁷.0¹²,¹⁶]Heptadeca-1(17),2,8,10,12(16)-pentaene-4,5,6,9,11-pentol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062204232D          

 22 25  0  0  1  0            999 V2000
    2.3675   -4.5355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0872   -3.7596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2751   -3.6143    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9948   -2.8384    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5266   -2.2077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2463   -1.4318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342   -1.2866    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1539   -0.5107    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0976   -1.9173    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9098   -1.7721    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1827   -2.6932    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3492   -3.3239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -2.3529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8705   -1.7222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6826   -1.8674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9629   -2.6434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4311   -3.2741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7114   -4.0500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6190   -3.1289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7875   -2.6166    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0168   -1.8241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3340   -1.3611    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  6  0  0  0
  5 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  1  0  0  0  0
 17 19  2  0  0  0  0
 13 19  1  0  0  0  0
  2 19  1  0  0  0  0
 16 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 15 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0224102

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1C=C2[C@@H](N=C(O)C3=C(O)C4=C(OCO4)C=C23)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H13NO7/c16-6-1-5-4-2-7-13(22-3-21-7)11(18)8(4)14(20)15-9(5)12(19)10(6)17/h1-2,6,9-10,12,16-19H,3H2,(H,15,20)/t6-,9-,10-,12+/m1/s1

> <INCHI_KEY>
LZAZURSABQIKGB-CWLXEDRGSA-N

> <FORMULA>
C14H13NO7

> <MOLECULAR_WEIGHT>
307.258

> <EXACT_MASS>
307.069201763

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
29.113781647483922

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4R,5R,6S,7R)-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),2,8,10,12(16)-pentaene-4,5,6,9,11-pentol

> <JCHEM_LOGP>
-0.0960598153333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.795095251269453

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.87329623537111

> <JCHEM_PKA_STRONGEST_BASIC>
1.2911926886637741

> <JCHEM_POLAR_SURFACE_AREA>
131.97000000000003

> <JCHEM_REFRACTIVITY>
72.52890000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5R,6S,7R)-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),2,8,10,12(16)-pentaene-4,5,6,9,11-pentol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  O   UNK     0       4.419  -8.466   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.896  -7.018   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.380  -6.747   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.857  -5.298   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.850  -4.121   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.326  -2.673   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.810  -2.402   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.287  -0.953   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.182  -3.579   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.698  -3.308   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.341  -5.027   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.652  -6.205   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.366  -4.392   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.358  -3.215   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.874  -3.486   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.398  -4.934   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.405  -6.112   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.928  -7.560   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.889  -5.841   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.937  -4.884   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.365  -3.405   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       8.090  -2.541   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4   12                                                  
CONECT   12   11                                                            
CONECT   13    5   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17   20                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   13    2                                                  
CONECT   20   16   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   15                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₁₃NO₇

Average Mass

307.2580 Da

Monoisotopic Mass

307.06920 Da

IUPAC Name

(4R,5R,6S,7R)-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),2,8,10,12(16)-pentaene-4,5,6,9,11-pentol

Traditional Name

(4R,5R,6S,7R)-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(17),2,8,10,12(16)-pentaene-4,5,6,9,11-pentol

CAS Registry Number

Not Available

SMILES

O[C@@H]1C=C2[C@@H](N=C(O)C3=C(O)C4=C(OCO4)C=C23)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C14H13NO7/c16-6-1-5-4-2-7-13(22-3-21-7)11(18)8(4)14(20)15-9(5)12(19)10(6)17/h1-2,6,9-10,12,16-19H,3H2,(H,15,20)/t6-,9-,10-,12+/m1/s1

InChI Key

LZAZURSABQIKGB-CWLXEDRGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Lycoris radiata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthridine- and phenanthridone-type amaryllidaceae alkaloids. These are amaryllidaceae alkaloids compounds based on the phenanthridine or the phenanthridone skeleton. Phenanthridone-type alkaloids have the highest oxygenated C ring in all Amaryllidaceae alkaloids, and they always show an amide group in ring B. On the contrary, alkaloids of the phenanthridine type often show completely aromatic ring system, occasionally with a methylation quaternary nitrogen atom.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Amaryllidaceae alkaloids

Sub Class

Phenanthridine- and phenanthridone-type amaryllidaceae alkaloids

Direct Parent

Phenanthridine- and phenanthridone-type amaryllidaceae alkaloids

Alternative Parents

Substituents

Phenanthridone-type amaryllidaceae alkaloid
Benzoquinoline
Phenanthridine
Isoquinolone
Quinoline
Tetrahydroisoquinoline
Benzodioxole
1-hydroxy-4-unsubstituted benzenoid
Cyclitol or derivatives
Benzenoid
Vinylogous acid
Carboxamide group
Lactam
Secondary carboxylic acid amide
Secondary alcohol
Acetal
Carboxylic acid derivative
Oxacycle
Azacycle
Polyol
Organoheterocyclic compound
Hydrocarbon derivative
Alcohol
Organic oxide
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organopnictogen 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	-0.096	ChemAxon
pKa (Strongest Acidic)	6.87	ChemAxon
pKa (Strongest Basic)	1.29	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	131.97 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	72.53 m³·mol⁻¹	ChemAxon
Polarizability	29.11 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

51351537

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol (NP0224102)

MOL for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

3D MOL for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

3D SDF for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

3D-SDF for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

PDB for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

3D PDB for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

SMILES for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

INCHI for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

Structure for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)

3D Structure for NP0224102 ((2r,3r,4s,4ar)-2h,3h,4h,4ah,9h-[1,3]dioxolo[4,5-j]phenanthridine-2,3,4,6,7-pentol)