NP-MRD: Showing NP-Card for Lycoricidinol (NP0050742)

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Record Information

Version

2.0

Created at

2022-04-27 22:04:47 UTC

Updated at

2022-04-27 22:04:47 UTC

NP-MRD ID

NP0050742

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lycoricidinol

Description

Narciclasine 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. Lycoricidinol is found in Brachystola magna, Haemanthus kalbreyeri, Hymenocallis littoralis, Lycoris longituba, Lycoris radiata , Lycoris sanguinea, Lycoris squamigera, Lycoris traubii, Narcissus cyclamineus, Narcissus jonquilla, Narcissus poeticus, Narcissus pseudonarcissus, Narcissus spp., Narcissus tarzettus and Sternbergia lutea. Lycoricidinol was first documented in 2021 (PMID: 35295737). Based on a literature review a small amount of articles have been published on Narciclasine (PMID: 35355337) (PMID: 35414025) (PMID: 35248554) (PMID: 35193667).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200042D          

 22 25  0  0  1  0            999 V2000
    3.9629    0.9934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4311    1.6241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6190    1.4789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387    0.7029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8705    0.0722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6826    0.2174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3340   -0.2889    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0168    0.1741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7875    0.9666    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5266    0.5577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2463   -0.2182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342   -0.3634    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0976    0.2673    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1827    1.0432    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9948    1.1884    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2751    1.9643    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0872    2.1096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3675    2.8855    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3492    1.6739    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9098    0.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1539   -1.1393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7114    2.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  4 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
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
  3 17  1  0  0  0  0
 17 18  2  0  0  0  0
 14 19  1  1  0  0  0
 13 20  1  1  0  0  0
 12 21  1  6  0  0  0
  2 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050742

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1C=C2[C@@H](NC(=O)C3=C2C=C2OCOC2=C3O)[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-/m0/s1

> <INCHI_KEY>
LZAZURSABQIKGB-AEKGRLRDSA-N

> <FORMULA>
C14H13NO7

> <MOLECULAR_WEIGHT>
307.258

> <EXACT_MASS>
307.069201763

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
28.908062893885017

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.82

> <JCHEM_LOGP>
-0.9156639423333335

> <ALOGPS_LOGS>
-1.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.87220264931057

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.43784097984654

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5076826691143332

> <JCHEM_POLAR_SURFACE_AREA>
128.48000000000002

> <JCHEM_REFRACTIVITY>
72.0072

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.39e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       7.398   1.854   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.405   3.032   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.889   2.761   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.366   1.312   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.358   0.135   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.874   0.406   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.090  -0.539   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.365   0.325   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.937   1.804   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.850   1.041   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.326  -0.407   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.810  -0.678   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.182   0.499   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.341   1.947   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.857   2.218   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       2.380   3.667   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       3.896   3.938   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.419   5.386   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.652   3.125   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -1.698   0.228   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.287  -2.127   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       6.928   4.480   0.000  0.00  0.00           O+0
CONECT    1    2    6    9                                                  
CONECT    2    1    3   22                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    1                                                       
CONECT   10    4   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14   20                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   10   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16    3   18                                                  
CONECT   18   17                                                            
CONECT   19   14                                                            
CONECT   20   13                                                            
CONECT   21   12                                                            
CONECT   22    2                                                            
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

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

O[C@H]1C=C2[C@@H](NC(=O)C3=C2C=C2OCOC2=C3O)[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-/m0/s1

InChI Key

LZAZURSABQIKGB-AEKGRLRDSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Brachystola magna	-	KNApSAcK
Haemanthus kalbreyeri	Plant	KNApSAcK
Hymenocallis littoralis	LOTUS Database	35616633
Lycoris longituba	Plant	KNApSAcK
Lycoris radiata	Plant	KNApSAcK
Lycoris sanguinea	Plant	KNApSAcK
Lycoris squamigera	LOTUS Database	35616633
Lycoris traubii	LOTUS Database	35616633
Narcissus cyclamineus	Plant	KNApSAcK
Narcissus jonquilla	Plant	KNApSAcK
Narcissus poeticus	Plant	KNApSAcK
Narcissus pseudonarcissus	Plant	KNApSAcK
Narcissus spp.	Plant	KNApSAcK
Narcissus tarzettus	Plant	KNApSAcK
Sternbergia lutea	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
Dihydroisoquinoline
Benzodioxole
1-hydroxy-4-unsubstituted benzenoid
Cyclitol or derivatives
Benzenoid
Cyclic carboximidic acid
Secondary alcohol
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Acetal
Oxacycle
Alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

phenanthridines (CHEBI:70169 )

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	-0.82	ALOGPS
logP	-0.92	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	8.44	ChemAxon
pKa (Strongest Basic)	-1.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	128.48 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	72.01 m³·mol⁻¹	ChemAxon
Polarizability	28.91 Å³	ChemAxon
Number of Rings	4	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

C00001577

Chemspider ID

65310

KEGG Compound ID

C08533

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Narciclasine

METLIN ID

Not Available

PubChem Compound

72376

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gonzalez BL, de Oliveira NC, Ritter MR, Tonin FS, Melo EB, Sanches ACC, Fernandez-Llimos F, Petruco MV, de Mello JCP, Chierrito D, de Medeiros Araujo DC: The naturally-derived alkaloids as a potential treatment for COVID-19: A scoping review. Phytother Res. 2022 Mar 30. doi: 10.1002/ptr.7442. [PubMed:35355337 ]
Pushparaj PN, Kalamegam G, Wali Sait KH, Rasool M: Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer's Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia. Front Pharmacol. 2022 Feb 28;12:720170. doi: 10.3389/fphar.2021.720170. eCollection 2021. [PubMed:35295737 ]
Liao M, Qin R, Huang W, Zhu HP, Peng F, Han B, Liu B: Targeting regulated cell death (RCD) with small-molecule compounds in triple-negative breast cancer: a revisited perspective from molecular mechanisms to targeted therapies. J Hematol Oncol. 2022 Apr 12;15(1):44. doi: 10.1186/s13045-022-01260-0. [PubMed:35414025 ]
Qiu Y, Fang B, Thuy NTT, Li A, Yoo HM, Zheng X, Cho N: Narciclasine suppresses esophageal cancer cell proliferation and migration by inhibiting the FAK signaling pathway. Eur J Pharmacol. 2022 Apr 15;921:174669. doi: 10.1016/j.ejphar.2021.174669. Epub 2022 Mar 3. [PubMed:35248554 ]
de Castro Barbosa E, Alves TMA, Kohlhoff M, Jangola STG, Pires DEV, Figueiredo ACC, Alves EAR, Calzavara-Silva CE, Sobral M, Kroon EG, Rosa LH, Zani CL, de Oliveira JG: Searching for plant-derived antivirals against dengue virus and Zika virus. Virol J. 2022 Feb 22;19(1):31. doi: 10.1186/s12985-022-01751-z. [PubMed:35193667 ]

Showing NP-Card for Lycoricidinol (NP0050742)

MOL for NP0050742 (Lycoricidinol)

3D MOL for NP0050742 (Lycoricidinol)

3D SDF for NP0050742 (Lycoricidinol)

3D-SDF for NP0050742 (Lycoricidinol)

PDB for NP0050742 (Lycoricidinol)

3D PDB for NP0050742 (Lycoricidinol)

SMILES for NP0050742 (Lycoricidinol)

INCHI for NP0050742 (Lycoricidinol)

Structure for NP0050742 (Lycoricidinol)

3D Structure for NP0050742 (Lycoricidinol)