NP-MRD: Showing NP-Card for fagaridine (NP0353371)

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Record Information

Version

2.0

Created at

2026-02-20 22:51:44 UTC

Updated at

2026-02-21 00:01:16 UTC

NP-MRD ID

NP0353371

Natural Product DOI

https://doi.org/10.57994/7845

Secondary Accession Numbers

None

Natural Product Identification

Common Name

fagaridine

Description

{18-Methoxy-21-methyl-5,7-dioxa-21λ⁵-azapentacyclo[11.8.0.0²,¹⁰.0⁴,⁸.0¹⁴,¹⁹]Henicosa-1(21),2,4(8),9,11,13,15,18,20-nonaen-17-ylidene}oxidanium belongs to the class of organic compounds known as quaternary benzophenanthridine alkaloids. These are alkaloids containing a quaternary N-demethylbenzophenanthridine skeleton, where the nitrogen atom of the phenanthridine moiety is part of four bonds. fagaridine was first documented in 2020 (PMID: 33001647). {18-Methoxy-21-methyl-5,7-dioxa-21λ⁵-azapentacyclo[11.8.0.0²,¹⁰.0⁴,⁸.0¹⁴,¹⁹]Henicosa-1(21),2,4(8),9,11,13,15,18,20-nonaen-17-ylidene}oxidanium is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004171519482D          

 25 29  0  0  0  0            999 V2000
    2.3706   -3.8846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1648   -3.6614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3686   -2.8619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7781   -2.2857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9839   -2.5090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9819   -1.4863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7761   -1.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3666   -1.8393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1608   -1.6160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3646   -0.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1588   -0.5934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7493   -1.1696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5435   -0.9463    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1339   -1.5225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9572   -1.4693    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2622   -2.2359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6275   -2.7628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9301   -2.3220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1359   -2.5452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5455   -1.9690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7512   -2.1922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5475   -2.9917    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    6.1379   -3.5679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7532   -3.2149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1628   -2.6387    0.0000 C   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  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 14 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 12 20  1  0  0  0  0
 20 21  1  0  0  0  0
  9 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 24 25  1  0  0  0  0
  3 25  2  0  0  0  0
  8 25  1  0  0  0  0
M  CHG  1  22   1
M  END


  Mrv1533004171519482D          

 25 29  0  0  0  0            999 V2000
    2.3706   -3.8846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1648   -3.6614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3686   -2.8619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7781   -2.2857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9839   -2.5090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9819   -1.4863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7761   -1.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3666   -1.8393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1608   -1.6160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3646   -0.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1588   -0.5934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7493   -1.1696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5435   -0.9463    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1339   -1.5225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9572   -1.4693    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2622   -2.2359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6275   -2.7628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9301   -2.3220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1359   -2.5452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5455   -1.9690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7512   -2.1922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5475   -2.9917    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    6.1379   -3.5679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7532   -3.2149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1628   -2.6387    0.0000 C   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  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 14 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 12 20  1  0  0  0  0
 20 21  1  0  0  0  0
  9 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 24 25  1  0  0  0  0
  3 25  2  0  0  0  0
  8 25  1  0  0  0  0
M  CHG  1  22   1
M  END
> <DATABASE_ID>
NP0353371

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C2C=[N+](C)C3=C(C=CC4=CC5=C(OCO5)C=C34)C2=CC=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C20H15NO4/c1-21-9-15-12(5-6-16(22)20(15)23-2)13-4-3-11-7-17-18(25-10-24-17)8-14(11)19(13)21/h3-9H,10H2,1-2H3/p+1

> <INCHI_KEY>
TXASKRGBMHFMPT-UHFFFAOYSA-O

> <FORMULA>
C20H16NO4

> <MOLECULAR_WEIGHT>
334.35

> <EXACT_MASS>
334.107384419

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
35.88550032854515

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
17-hydroxy-18-methoxy-21-methyl-5,7-dioxa-21-azapentacyclo[11.8.0.0²,¹⁰.0⁴,⁸.0¹⁴,¹⁹]henicosa-1(13),2,4(8),9,11,14,16,18,20-nonaen-21-ium

> <ALOGPS_LOGP>
-0.21

> <JCHEM_LOGP>
-1.0279666968050791

> <ALOGPS_LOGS>
-6.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.826407940474363

> <JCHEM_PKA_STRONGEST_BASIC>
-4.539695403771604

> <JCHEM_POLAR_SURFACE_AREA>
51.800000000000004

> <JCHEM_REFRACTIVITY>
93.4956

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.98e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
17-hydroxy-18-methoxy-21-methyl-5,7-dioxa-21-azapentacyclo[11.8.0.0²,¹⁰.0⁴,⁸.0¹⁴,¹⁹]henicosa-1(13),2,4(8),9,11,14,16,18,20-nonaen-21-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       4.425  -7.251   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       5.908  -6.835   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.288  -5.342   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.186  -4.267   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.703  -4.683   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.566  -2.774   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.049  -2.358   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.151  -3.433   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.633  -3.017   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.014  -1.524   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.496  -1.108   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.599  -2.183   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.081  -1.766   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      15.183  -2.842   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      16.720  -2.743   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      17.289  -4.174   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      16.105  -5.157   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      14.803  -4.334   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.320  -4.751   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.218  -3.675   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.736  -4.092   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0      10.355  -5.584   0.000  0.00  0.00           N+1
HETATM   23  C   UNK     0      11.457  -6.660   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.873  -6.001   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.771  -4.926   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   25                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   25                                                  
CONECT    9    8   10   21                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   20                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   14   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   12   21                                                  
CONECT   21   20    9   22                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24    3    8                                                  
MASTER        0    0    0    0    0    0    0    0   25    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₁₆NO₄

Average Mass

334.3500 Da

Monoisotopic Mass

334.10738 Da

IUPAC Name

17-hydroxy-18-methoxy-21-methyl-5,7-dioxa-21-azapentacyclo[11.8.0.0²,¹⁰.0⁴,⁸.0¹⁴,¹⁹]henicosa-1(13),2,4(8),9,11,14,16,18,20-nonaen-21-ium

Traditional Name

17-hydroxy-18-methoxy-21-methyl-5,7-dioxa-21-azapentacyclo[11.8.0.0²,¹⁰.0⁴,⁸.0¹⁴,¹⁹]henicosa-1(13),2,4(8),9,11,14,16,18,20-nonaen-21-ium

CAS Registry Number

Not Available

SMILES

COC1=C2C=[N+](C)C3=C(C=CC4=CC5=C(OCO5)C=C34)C2=CC=C1O

InChI Identifier

InChI=1S/C20H15NO4/c1-21-9-15-12(5-6-16(22)20(15)23-2)13-4-3-11-7-17-18(25-10-24-17)8-14(11)19(13)21/h3-9H,10H2,1-2H3/p+1

InChI Key

TXASKRGBMHFMPT-UHFFFAOYSA-O

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500.13, Dimethylsulfoxide-d6, simulated)	[email protected]	Not Available	Not Available	2026-02-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125.77, Dimethylsulfoxide-d6, simulated)	[email protected]	Not Available	Not Available	2026-02-20	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Toddalia asiatica		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as quaternary benzophenanthridine alkaloids. These are alkaloids containing a quaternary N-demethylbenzophenanthridine skeleton, where the nitrogen atom of the phenanthridine moiety is part of four bonds.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Benzophenanthridine alkaloids

Sub Class

Quaternary benzophenanthridine alkaloids

Direct Parent

Quaternary benzophenanthridine alkaloids

Alternative Parents

Substituents

Quaternary benzophenanthridine alkaloid skeleton
Benzoquinoline
Phenanthridine
Isoquinoline
Naphthalene
Quinoline
Benzodioxole
Anisole
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Pyridine
Pyridinium
Heteroaromatic compound
Acetal
Ether
Oxacycle
Azacycle
Organoheterocyclic compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Organic cation
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	-0.21	ALOGPS
logP	-1	ChemAxon
logS	-6.1	ALOGPS
pKa (Strongest Acidic)	8.83	ChemAxon
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	51.8 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	93.5 m³·mol⁻¹	ChemAxon
Polarizability	35.89 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

5318563

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

DOI: 10.1021/acs.jnatprod.0c00564

Showing NP-Card for fagaridine (NP0353371)

MOL for NP0353371 (fagaridine)

3D MOL for NP0353371 (fagaridine)

3D SDF for NP0353371 (fagaridine)

3D-SDF for NP0353371 (fagaridine)

PDB for NP0353371 (fagaridine)

3D PDB for NP0353371 (fagaridine)

SMILES for NP0353371 (fagaridine)

INCHI for NP0353371 (fagaridine)

Structure for NP0353371 (fagaridine)

3D Structure for NP0353371 (fagaridine)