NP-MRD: Showing NP-Card for zephycitrine (NP0333726)

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Record Information

Version

2.0

Created at

2024-08-12 09:45:13 UTC

Updated at

2025-12-20 13:41:06 UTC

NP-MRD ID

NP0333726

Natural Product DOI

https://doi.org/10.57994/3205

Secondary Accession Numbers

None

Natural Product Identification

Common Name

zephycitrine

Description

Zephycitrine 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. zephycitrine was first documented in 2024 (PMID: 39229678). Based on a literature review very few articles have been published on zephycitrine.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 04262312182D          

 24 27  0  0  1  0            999 V2000
    1.1535    1.5006    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3293    1.4643    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4731    1.6560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0404    1.0569    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8428    1.2486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4100    0.6496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8052    0.2662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0028    0.0744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5645    0.6735    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3971    0.7674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8914    0.1069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7106    0.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2049   -0.4558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8801   -1.2141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0354    0.9631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8546    1.0609    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1794    1.8193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5411    1.6236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7219    1.5257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3315    2.2525    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5199    2.4005    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1018    1.8581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0654    1.0339    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7698    0.6044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  1  0  0  0
  5  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  2  0  0  0  0
  9  8  1  1  0  0  0
  9  2  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  1  0  0  0  0
 13 14  1  0  0  0  0
 12 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  2  0  0  0  0
 10 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
  2 21  1  0  0  0  0
 21 22  1  0  0  0  0
 23 22  1  0  0  0  0
  9 23  1  0  0  0  0
 23 24  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0333726

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@H](OC)C=C[C@@]11[C@@H](O)CN2CC2=CC(OC)=C(OC)C=C12

> <INCHI_IDENTIFIER>
InChI=1S/C18H23NO4/c1-21-12-4-5-18-13-8-15(23-3)14(22-2)6-11(13)9-19(10-17(18)20)16(18)7-12/h4-6,8,12,16-17,20H,7,9-10H2,1-3H3/t12-,16+,17+,18+/m1/s1

> <INCHI_KEY>
LIDPBBPVLVYZHF-IEGACIPQSA-N

> <FORMULA>
C18H23NO4

> <MOLECULAR_WEIGHT>
317.385

> <EXACT_MASS>
317.162708225

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
34.65667096668333

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,10S,12S,15R)-4,5,12-trimethoxy-9-azatetracyclo[7.5.2.0^{1,10}.0^{2,7}]hexadeca-2,4,6,13-tetraen-15-ol

> <JCHEM_LOGP>
0.8871731603333336

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.129298053011022

> <JCHEM_PKA_STRONGEST_BASIC>
8.521928275020146

> <JCHEM_POLAR_SURFACE_AREA>
51.16

> <JCHEM_REFRACTIVITY>
88.26359999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,10S,12S,15R)-4,5,12-trimethoxy-9-azatetracyclo[7.5.2.0^{1,10}.0^{2,7}]hexadeca-2,4,6,13-tetraen-15-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-APR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-23         0                                  
HETATM    1  H   UNK     0       2.153   2.801   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       0.615   2.733   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.883   3.091   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.942   1.973   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.440   2.331   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.499   1.213   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.503   0.497   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.005   0.139   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.054   1.257   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.608   1.432   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.531   0.199   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.060   0.382   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.983  -0.851   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.376  -2.266   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.666   1.798   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       7.195   1.980   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       7.802   3.396   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.743   3.031   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.214   2.848   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.486   4.205   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       0.971   4.481   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      -0.190   3.469   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.122   1.930   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.437   1.128   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9   21                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    2   10   23                                             
CONECT   10    9   11   19                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19                                                       
CONECT   19   18   10   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20    2   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22    9   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₂₃NO₄

Average Mass

317.3850 Da

Monoisotopic Mass

317.16271 Da

IUPAC Name

(1S,10S,12S,15R)-4,5,12-trimethoxy-9-azatetracyclo[7.5.2.0^{1,10}.0^{2,7}]hexadeca-2,4,6,13-tetraen-15-ol

Traditional Name

(1S,10S,12S,15R)-4,5,12-trimethoxy-9-azatetracyclo[7.5.2.0^{1,10}.0^{2,7}]hexadeca-2,4,6,13-tetraen-15-ol

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@H](OC)C=C[C@@]11[C@@H](O)CN2CC2=CC(OC)=C(OC)C=C12

InChI Identifier

InChI=1S/C18H23NO4/c1-21-12-4-5-18-13-8-15(23-3)14(22-2)6-11(13)9-19(10-17(18)20)16(18)7-12/h4-6,8,12,16-17,20H,7,9-10H2,1-3H3/t12-,16+,17+,18+/m1/s1

InChI Key

LIDPBBPVLVYZHF-IEGACIPQSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCL3, experimental)	[email protected]	Faculty of Pharmacy, Charles University	Jana Křoustková	2024-08-12	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCL3, experimental)	[email protected]	Faculty of Pharmacy, Charles University	Jana Křoustková	2024-08-12	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCL3, experimental)	[email protected]	Faculty of Pharmacy, Charles University	Jana Křoustková	2024-08-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCL3, experimental)	[email protected]	Faculty of Pharmacy, Charles University	Jana Křoustková	2024-08-12	View Spectrum
H2BC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCL3, experimental)	[email protected]	Faculty of Pharmacy, Charles University	Jana Křoustková	2024-08-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CDCL3, experimental)	[email protected]	Faculty of Pharmacy, Charles University	Jana Křoustková	2024-08-12	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCL3, experimental)	[email protected]	Faculty of Pharmacy, Charles University	Jana Křoustková	2024-08-12	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Zephyranthes citrina		Not Available

Chemical Taxonomy

Description

This compound 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
Benzazepine
Tetrahydroisoquinoline
Indole or derivatives
Anisole
Aralkylamine
Azepine
Azepane
Alkyl aryl ether
Benzenoid
N-alkylpyrrolidine
Piperidine
Pyrrolidine
1,3-aminoalcohol
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Azacycle
Ether
Dialkyl ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Amine
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	0.89	ChemAxon
pKa (Strongest Acidic)	14.13	ChemAxon
pKa (Strongest Basic)	8.52	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	51.16 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	88.26 m³·mol⁻¹	ChemAxon
Polarizability	34.66 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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kroustkova J, Kohelova E, Muthna D, Kunes J, Havelek R, Vrabec R, Malanik M, Suchankova D, Chlebek J, Jenco J, Kosturko S, Cahlikova L: Undescribed Amaryllidaceae Alkaloids from Zephyranthes citrina and Their Cytotoxicity. J Nat Prod. 2024 Sep 27;87(9):2317-2326. doi: 10.1021/acs.jnatprod.4c00825. Epub 2024 Sep 4. [PubMed:39229678 ]
DOI: 10.1021/acs.jnatprod.4c00825
PMID: 39229678

Showing NP-Card for zephycitrine (NP0333726)

MOL for NP0333726 (zephycitrine)

3D MOL for NP0333726 (zephycitrine)

3D SDF for NP0333726 (zephycitrine)

3D-SDF for NP0333726 (zephycitrine)

PDB for NP0333726 (zephycitrine)

3D PDB for NP0333726 (zephycitrine)

SMILES for NP0333726 (zephycitrine)

INCHI for NP0333726 (zephycitrine)

Structure for NP0333726 (zephycitrine)

3D Structure for NP0333726 (zephycitrine)