NP-MRD: Showing NP-Card for (+)-Pancratistatin (NP0050744)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-27 22:04:53 UTC

Updated at

2022-04-27 22:04:53 UTC

NP-MRD ID

NP0050744

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Pancratistatin

Description

Pancratistatin 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. (+)-Pancratistatin is found in Brachystola magna, Delphinium denudatum, Delphinium denudatum Wall. , Hymenocallis expansa, Hymenocallis litroralis, Hymenocallis littorale, Hymenocallis littoralis , Hymenocallis sonorensis, Hymenocallis speciosa, Pancratium maritimum, Habranthus brachyandrus, Zephyranthes carinata and Zephyranthes grandiflora . (+)-Pancratistatin was first documented in 2019 (PMID: 31542397). Based on a literature review a small amount of articles have been published on Pancratistatin (PMID: 35357593) (PMID: 35214809) (PMID: 33820903) (PMID: 31823643).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200042D          

 23 26  0  0  1  0            999 V2000
    3.9629   -0.1684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4311   -0.7991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6190   -0.6539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387    0.1221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8705    0.7528    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6826    0.6076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3340    1.1139    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0168    0.6509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7875   -0.1416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5266    0.2673    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9948   -0.3634    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2751   -1.1393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0872   -1.2846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3675   -2.0605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1827   -0.2182    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0976    0.5577    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4342    1.1884    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2463    1.0432    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7781    1.6739    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1539    1.9643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9098    0.7029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3492   -0.8489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7114   -1.5750    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
 10  4  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
  3 13  1  0  0  0  0
 13 14  2  0  0  0  0
 11 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
 10 18  1  0  0  0  0
 18 19  1  6  0  0  0
 17 20  1  1  0  0  0
 16 21  1  6  0  0  0
 15 22  1  6  0  0  0
  2 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050744

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H](O)[C@H](O)[C@H]2[C@@H](NC(=O)C3=C2C=C2OCOC2=C3O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H15NO8/c16-8-5-3-1-4-13(23-2-22-4)9(17)6(3)14(21)15-7(5)10(18)12(20)11(8)19/h1,5,7-8,10-12,16-20H,2H2,(H,15,21)/t5-,7-,8-,10+,11+,12+/m1/s1

> <INCHI_KEY>
VREZDOWOLGNDPW-ALTGWBOUSA-N

> <FORMULA>
C14H15NO8

> <MOLECULAR_WEIGHT>
325.273

> <EXACT_MASS>
325.079766447

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
30.335210283175076

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6S,7R)-3,4,5,6,11-pentahydroxy-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),11,16-trien-9-one

> <ALOGPS_LOGP>
-1.59

> <JCHEM_LOGP>
-1.9160258643333337

> <ALOGPS_LOGS>
-0.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.685454372218988

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.476215209500412

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3331945337257642

> <JCHEM_POLAR_SURFACE_AREA>
148.71

> <JCHEM_REFRACTIVITY>
72.6509

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.46e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6S,7R)-3,4,5,6,11-pentahydroxy-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),11,16-trien-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  -0.314   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.405  -1.492   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.889  -1.221   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.366   0.228   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.358   1.405   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.874   1.134   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.090   2.079   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.365   1.215   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.937  -0.264   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.850   0.499   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.857  -0.678   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.380  -2.127   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       3.896  -2.398   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.419  -3.846   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.341  -0.407   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.182   1.041   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.810   2.218   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.326   1.947   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.319   3.125   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.287   3.667   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -1.698   1.312   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -0.652  -1.585   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.928  -2.940   0.000  0.00  0.00           O+0
CONECT    1    2    6    9                                                  
CONECT    2    1    3   23                                                  
CONECT    3    2    4   13                                                  
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   18                                                  
CONECT   11   10   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12    3   14                                                  
CONECT   14   13                                                            
CONECT   15   11   16   22                                                  
CONECT   16   15   17   21                                                  
CONECT   17   16   18   20                                                  
CONECT   18   17   10   19                                                  
CONECT   19   18                                                            
CONECT   20   17                                                            
CONECT   21   16                                                            
CONECT   22   15                                                            
CONECT   23    2                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₁₅NO₈

Average Mass

325.2730 Da

Monoisotopic Mass

325.07977 Da

IUPAC Name

(2R,3R,4S,5S,6S,7R)-3,4,5,6,11-pentahydroxy-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),11,16-trien-9-one

Traditional Name

(2R,3R,4S,5S,6S,7R)-3,4,5,6,11-pentahydroxy-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),11,16-trien-9-one

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](O)[C@H](O)[C@H]2[C@@H](NC(=O)C3=C2C=C2OCOC2=C3O)[C@@H]1O

InChI Identifier

InChI=1S/C14H15NO8/c16-8-5-3-1-4-13(23-2-22-4)9(17)6(3)14(21)15-7(5)10(18)12(20)11(8)19/h1,5,7-8,10-12,16-20H,2H2,(H,15,21)/t5-,7-,8-,10+,11+,12+/m1/s1

InChI Key

VREZDOWOLGNDPW-ALTGWBOUSA-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
Delphinium denudatum	LOTUS Database	35616633
Delphinium denudatum Wall.	Plant	KNApSAcK
Hymenocallis expansa	Plant	KNApSAcK
Hymenocallis litroralis	Plant	KNApSAcK
Hymenocallis littorale	Plant	KNApSAcK
Hymenocallis littoralis	Plant	KNApSAcK
Hymenocallis sonorensis	Plant	KNApSAcK
Hymenocallis speciosa	Plant	KNApSAcK
Pancratium maritimum	LOTUS Database	35616633
Zephyranthes brachyandra	LOTUS Database	35616633
Zephyranthes carinata	LOTUS Database	35616633
Zephyranthes grandiflora	Plant	KNApSAcK

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
Cyclic alcohol
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Lactam
Oxacycle
Azacycle
Organoheterocyclic compound
Acetal
Polyol
Carboxylic acid derivative
Organic oxide
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organic nitrogen compound
Alcohol
Organopnictogen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

citraconoyl group (CHEBI:7906 )

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	-1.6	ALOGPS
logP	-1.9	ChemAxon
logS	-0.59	ALOGPS
pKa (Strongest Acidic)	8.48	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	148.71 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	72.65 m³·mol⁻¹	ChemAxon
Polarizability	30.34 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

C00001579

Chemspider ID

390265

KEGG Compound ID

C08535

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pancratistatin

METLIN ID

Not Available

PubChem Compound

441597

PDB ID

Not Available

ChEBI ID

7906

Good Scents ID

Not Available

References

General References

Rammohan A, Khasanov AF, Kopchuk DS, Gunasekar D, Zyryanov GV, Chupakhin ON: Assessment on facile Diels-Alder approach of alpha-pyrone and terpenoquinone for the expedient synthesis of various natural scaffolds. Nat Prod Bioprospect. 2022 Mar 31;12(1):12. doi: 10.1007/s13659-022-00333-4. [PubMed:35357593 ]
Youssef DTA, Shaala LA, Altyar AE: Cytotoxic Phenylpropanoid Derivatives and Alkaloids from the Flowers of Pancratium maritimum L. Plants (Basel). 2022 Feb 9;11(4). pii: plants11040476. doi: 10.3390/plants11040476. [PubMed:35214809 ]
Xiong Y, Xiong YJ, Liu DY, Shen RR: Retracted: Pancratistatin Inhibits the Growth of Colorectal Cancer Cells by Inducing Apoptosis, Autophagy, and G2/M Cell Cycle Arrest. Med Sci Monit. 2021 Mar 25;27:e932346. doi: 10.12659/MSM.932346. [PubMed:33820903 ]
Liang X, Zhang L, Li F, Luan S, He C, Yin L, Yin Z, Zou Y, Yue G, Li L, Song X, Lv C, Zhang W, Jing B: Autophagy-regulating N-heterocycles derivatives as potential anticancer agents. Future Med Chem. 2020 Feb;12(3):223-242. doi: 10.4155/fmc-2019-0294. Epub 2019 Dec 11. [PubMed:31823643 ]
Dutta P, Sahu RK, Dey T, Lahkar MD, Manna P, Kalita J: Beneficial role of insect-derived bioactive components against inflammation and its associated complications (colitis and arthritis) and cancer. Chem Biol Interact. 2019 Nov 1;313:108824. doi: 10.1016/j.cbi.2019.108824. Epub 2019 Sep 19. [PubMed:31542397 ]

Showing NP-Card for (+)-Pancratistatin (NP0050744)

MOL for NP0050744 ((+)-Pancratistatin)

3D MOL for NP0050744 ((+)-Pancratistatin)

3D SDF for NP0050744 ((+)-Pancratistatin)

3D-SDF for NP0050744 ((+)-Pancratistatin)

PDB for NP0050744 ((+)-Pancratistatin)

3D PDB for NP0050744 ((+)-Pancratistatin)

SMILES for NP0050744 ((+)-Pancratistatin)

INCHI for NP0050744 ((+)-Pancratistatin)

Structure for NP0050744 ((+)-Pancratistatin)

3D Structure for NP0050744 ((+)-Pancratistatin)