NP-MRD: Showing NP-Card for 1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin (NP0069457)

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Record Information

Version

2.0

Created at

2022-04-28 14:48:26 UTC

Updated at

2022-04-28 14:48:26 UTC

NP-MRD ID

NP0069457

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin

Description

(1R)-1beta-[[(3S)-3-(beta-D-Glucopyranosyloxy)butyryl]oxy]-2alpha,3beta,4beta,7-tetrahydroxy-2,3,4,4abeta,5,11balpha-hexahydro[1,3]dioxolo[4,5-j]phenanthridine-6(1H)-one 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. 1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin is found in Zephyranthes carinata . Based on a literature review very few articles have been published on (1R)-1beta-[[(3S)-3-(beta-D-Glucopyranosyloxy)butyryl]oxy]-2alpha,3beta,4beta,7-tetrahydroxy-2,3,4,4abeta,5,11balpha-hexahydro[1,3]dioxolo[4,5-j]phenanthridine-6(1H)-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282216482D          

 40 44  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282216482D          

 40 44  0  0  1  0            999 V2000
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    2.9282   -5.3650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2085   -6.1409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5524   -5.6554    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6161   -4.3940    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0555   -2.8422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7752   -2.0662    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
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  5  8  1  6  0  0  0
  4  9  1  6  0  0  0
  3 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
  2 14  1  6  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  2  0  0  0  0
 13 18  1  0  0  0  0
 18 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 16 22  1  0  0  0  0
  1 23  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 29 28  1  1  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 29 34  1  0  0  0  0
 33 35  1  1  0  0  0
 35 36  1  0  0  0  0
 32 37  1  6  0  0  0
 31 38  1  1  0  0  0
 30 39  1  6  0  0  0
 27 40  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0069457

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](CC(=O)O[C@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@@H]2NC(=O)C3=C(C=C4OCOC4=C3O)[C@@H]12)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H31NO15/c1-6(38-24-20(34)17(31)14(28)9(4-26)39-24)2-10(27)40-22-11-7-3-8-21(37-5-36-8)15(29)12(7)23(35)25-13(11)16(30)18(32)19(22)33/h3,6,9,11,13-14,16-20,22,24,26,28-34H,2,4-5H2,1H3,(H,25,35)/t6-,9+,11+,13+,14+,16-,17-,18-,19+,20+,22+,24+/m0/s1

> <INCHI_KEY>
QGRGVCXBYQUGHI-PKUULSAOSA-N

> <FORMULA>
C24H31NO15

> <MOLECULAR_WEIGHT>
573.504

> <EXACT_MASS>
573.169369302

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
53.25701214896009

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5S,6S,7R)-4,5,6,11-tetrahydroxy-9-oxo-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),11,16-trien-3-yl (3S)-3-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanoate

> <ALOGPS_LOGP>
-1.56

> <JCHEM_LOGP>
-3.4093963846666657

> <ALOGPS_LOGS>
-1.21

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.094271036899437

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.47606169913384

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4583951707110128

> <JCHEM_POLAR_SURFACE_AREA>
254.1599999999999

> <JCHEM_REFRACTIVITY>
125.03609999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.51e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5S,6S,7R)-4,5,6,11-tetrahydroxy-9-oxo-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),11,16-trien-3-yl (3S)-3-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanoate

> <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       8.337   1.666   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.813   3.114   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.806   4.291   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.322   4.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.845   2.572   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.853   1.394   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      10.376  -0.054   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      12.361   2.301   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      11.315   5.197   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       8.283   5.740   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       6.767   6.011   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.244   7.459   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.774   4.833   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.297   3.385   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.305   2.208   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.789   2.479   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.266   3.927   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.258   5.104   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.735   6.553   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.726   3.877   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.298   2.398   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.573   1.534   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       7.344   0.488   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       7.867  -0.960   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       9.383  -1.231   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       6.874  -2.138   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.398  -3.586   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       6.405  -4.763   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       6.928  -6.212   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.444  -6.483   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.967  -7.931   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.975  -9.108   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.459  -8.837   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       5.935  -7.389   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       5.466 -10.015   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       5.989 -11.463   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       8.498 -10.557   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      10.483  -8.202   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       9.437  -5.305   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       8.914  -3.857   0.000  0.00  0.00           C+0
CONECT    1    2    6   23                                                  
CONECT    2    1    3   14                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    4                                                            
CONECT   10    3   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   18                                                  
CONECT   14   13    2   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   22                                                  
CONECT   17   16   18   20                                                  
CONECT   18   17   13   19                                                  
CONECT   19   18                                                            
CONECT   20   17   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   16                                                       
CONECT   23    1   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28   40                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   34                                                  
CONECT   30   29   31   39                                                  
CONECT   31   30   32   38                                                  
CONECT   32   31   33   37                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33   29                                                       
CONECT   35   33   36                                                       
CONECT   36   35                                                            
CONECT   37   32                                                            
CONECT   38   31                                                            
CONECT   39   30                                                            
CONECT   40   27                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Value	Source
(1R)-1b-[[(3S)-3-(b-D-Glucopyranosyloxy)butyryl]oxy]-2a,3b,4b,7-tetrahydroxy-2,3,4,4abeta,5,11balpha-hexahydro[1,3]dioxolo[4,5-J]phenanthridine-6(1H)-one	Generator
(1R)-1Β-[[(3S)-3-(β-D-glucopyranosyloxy)butyryl]oxy]-2α,3β,4β,7-tetrahydroxy-2,3,4,4abeta,5,11balpha-hexahydro[1,3]dioxolo[4,5-J]phenanthridine-6(1H)-one	Generator

Chemical Formula

C₂₄H₃₁NO₁₅

Average Mass

573.5040 Da

Monoisotopic Mass

573.16937 Da

IUPAC Name

(2R,3R,4R,5S,6S,7R)-4,5,6,11-tetrahydroxy-9-oxo-13,15-dioxa-8-azatetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),11,16-trien-3-yl (3S)-3-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanoate

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@@H](CC(=O)O[C@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@@H]2NC(=O)C3=C(C=C4OCOC4=C3O)[C@@H]12)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C24H31NO15/c1-6(38-24-20(34)17(31)14(28)9(4-26)39-24)2-10(27)40-22-11-7-3-8-21(37-5-36-8)15(29)12(7)23(35)25-13(11)16(30)18(32)19(22)33/h3,6,9,11,13-14,16-20,22,24,26,28-34H,2,4-5H2,1H3,(H,25,35)/t6-,9+,11+,13+,14+,16-,17-,18-,19+,20+,22+,24+/m0/s1

InChI Key

QGRGVCXBYQUGHI-PKUULSAOSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Zephyranthes carinata	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
Fatty acyl glycoside of mono- or disaccharide
Fatty acyl glycoside
Phenanthridine
Benzoquinoline
Hexose monosaccharide
O-glycosyl compound
Isoquinolone
Glycosyl compound
Tetrahydroisoquinoline
Quinoline
Benzodioxole
1-hydroxy-4-unsubstituted benzenoid
Sugar acid
Fatty acid ester
Fatty acyl
Benzenoid
Oxane
Monosaccharide
Cyclitol or derivatives
Vinylogous acid
Cyclic alcohol
Secondary carboxylic acid amide
Secondary alcohol
Lactam
Carboxylic acid ester
Carboxamide group
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
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	-1.6	ALOGPS
logP	-3.4	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	8.48	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	254.16 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	125.04 m³·mol⁻¹	ChemAxon
Polarizability	53.26 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

101147060

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin (NP0069457)

MOL for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

3D MOL for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

3D SDF for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

3D-SDF for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

PDB for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

3D PDB for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

SMILES for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

INCHI for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

Structure for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)

3D Structure for NP0069457 (1-O-(3-O-beta-D-glucopyranosylbutyryl)pancratistatin)