NP-MRD: Showing NP-Card for Podophyllotoxin 4-O-glucoside (NP0138526)

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Record Information

Version

2.0

Created at

2022-06-29 17:33:37 UTC

Updated at

2022-06-29 17:33:37 UTC

NP-MRD ID

NP0138526

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Podophyllotoxin 4-O-glucoside

Description

Podophyllotoxin 4-O-glucoside, also known as PGB or prostaglandins b, belongs to the class of organic compounds known as podophyllotoxins. These are tetralin lignans in which the benzene moiety of the tetralin skeleton is fused to a 1,3-dioxolane and the cyclohexane is fused to a butyrolactone (pyrrolidin-2-one). Podophyllotoxin 4-O-glucoside is found in Callitris drummondii, Libocedrus chevalieri, Linum cariense and Podophyllum peltatum. Podophyllotoxin 4-O-glucoside was first documented in 1990 (PMID: 24227060). Based on a literature review very few articles have been published on Podophyllotoxin 4-O-glucoside.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306292219332D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306292219332D          

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    1.2089    0.1271    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4944   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2201    0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4944    1.3646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    2.1896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.3646    0.0000 O   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13  5  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 14 18  1  1  0  0  0
 18 19  2  0  0  0  0
 15 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 13 26  1  0  0  0  0
 21 26  1  0  0  0  0
 24 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 23 29  1  0  0  0  0
 20 30  1  1  0  0  0
 31 30  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 31 36  1  0  0  0  0
 35 37  1  6  0  0  0
 37 38  1  0  0  0  0
 34 39  1  1  0  0  0
 33 40  1  6  0  0  0
 32 41  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0138526

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1OC)[C@H]1[C@@H]2[C@H](COC2=O)[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C2=CC3=C(OCO3)C=C12

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O13/c1-34-17-4-11(5-18(35-2)26(17)36-3)20-12-6-15-16(39-10-38-15)7-13(12)25(14-9-37-27(33)21(14)20)41-28-24(32)23(31)22(30)19(8-29)40-28/h4-7,14,19-25,28-32H,8-10H2,1-3H3/t14-,19+,20+,21-,22+,23-,24+,25-,28-/m0/s1

> <INCHI_KEY>
NXVJTGLCCSFGAT-QNDDJFOYSA-N

> <FORMULA>
C28H32O13

> <MOLECULAR_WEIGHT>
576.551

> <EXACT_MASS>
576.18429109

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
57.53586331089686

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(10R,11R,15R,16R)-16-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-10-(3,4,5-trimethoxyphenyl)-4,6,13-trioxatetracyclo[7.7.0.0^{3,7}.0^{11,15}]hexadeca-1,3(7),8-trien-12-one

> <ALOGPS_LOGP>
0.95

> <JCHEM_LOGP>
-0.14803737633333264

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.19989635096126

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210065094975828

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083687036146

> <JCHEM_POLAR_SURFACE_AREA>
171.82999999999998

> <JCHEM_REFRACTIVITY>
136.31830000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.99e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(10R,11R,15R,16R)-16-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-10-(3,4,5-trimethoxyphenyl)-4,6,13-trioxatetracyclo[7.7.0.0^{3,7}.0^{11,15}]hexadeca-1,3(7),8-trien-12-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0       3.590 -11.313   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       3.590  -9.773   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.924  -9.003   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924  -7.463   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258  -6.693   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.591  -7.463   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.591  -9.003   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.258  -9.773   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.258 -11.313   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       7.591 -12.083   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       8.925  -9.773   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       8.925 -11.313   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.258  -5.153   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.924  -4.383   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.459  -2.367   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.554  -3.613   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.459  -4.859   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.983  -6.323   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.591  -2.843   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.925  -2.073   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.259  -2.843   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.259  -4.383   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.925  -5.153   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.591  -4.383   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      11.723  -4.859   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      12.628  -3.613   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      11.723  -2.367   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       6.258  -0.533   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.924   1.777   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.590   2.547   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.257   1.777   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.257   0.237   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       3.590  -0.533   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       0.923  -0.533   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -0.411   0.237   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       0.923   2.547   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       3.590   4.087   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       6.258   2.547   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    3    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    7   12                                                       
CONECT   12   11                                                            
CONECT   13    5   14   26                                                  
CONECT   14   13   15   18                                                  
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   14   19                                                  
CONECT   19   18                                                            
CONECT   20   15   21   30                                                  
CONECT   21   20   22   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   29                                                  
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25   13   21                                                  
CONECT   27   24   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   23                                                       
CONECT   30   20   31                                                       
CONECT   31   30   32   36                                                  
CONECT   32   31   33   41                                                  
CONECT   33   32   34   40                                                  
CONECT   34   33   35   39                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35   31                                                       
CONECT   37   35   38                                                       
CONECT   38   37                                                            
CONECT   39   34                                                            
CONECT   40   33                                                            
CONECT   41   32                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   92    0
END

View in JSmol

Synonyms

Value	Source
PGB	MeSH
Prostaglandins b	MeSH

Chemical Formula

C₂₈H₃₂O₁₃

Average Mass

576.5510 Da

Monoisotopic Mass

576.18429 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

16481-54-2

SMILES

COC1=CC(=CC(OC)=C1OC)[C@H]1[C@@H]2[C@H](COC2=O)[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C2=CC3=C(OCO3)C=C12

InChI Identifier

InChI=1S/C28H32O13/c1-34-17-4-11(5-18(35-2)26(17)36-3)20-12-6-15-16(39-10-38-15)7-13(12)25(14-9-37-27(33)21(14)20)41-28-24(32)23(31)22(30)19(8-29)40-28/h4-7,14,19-25,28-32H,8-10H2,1-3H3/t14-,19+,20+,21-,22+,23-,24+,25-,28-/m0/s1

InChI Key

NXVJTGLCCSFGAT-QNDDJFOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Callitris drummondii	LOTUS Database	35616633
Libocedrus chevalieri	LOTUS Database	35616633
Linum cariense	LOTUS Database	35616633
Podophyllum peltatum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as podophyllotoxins. These are tetralin lignans in which the benzene moiety of the tetralin skeleton is fused to a 1,3-dioxolane and the cyclohexane is fused to a butyrolactone (pyrrolidin-2-one).

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Lignan lactones

Sub Class

Podophyllotoxins

Direct Parent

Podophyllotoxins

Alternative Parents

Substituents

Podophyllotoxin
Lignan glycoside
1-aryltetralin lignan
Linear furanonaphthodioxole
Naphthofuran
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Tetralin
Benzodioxole
Phenoxy compound
Anisole
Phenol ether
Methoxybenzene
Alkyl aryl ether
Gamma butyrolactone
Oxane
Monocyclic benzene moiety
Monosaccharide
Benzenoid
Oxolane
Secondary alcohol
Carboxylic acid ester
Lactone
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Polyol
Ether
Organoheterocyclic compound
Oxacycle
Primary alcohol
Carbonyl group
Organic oxygen compound
Organic oxide
Alcohol
Organooxygen compound
Hydrocarbon derivative
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

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

141589

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

161177

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Heyenga AG, Lucas JA, Dewick PM: Production of tumour-inhibitory lignans in callus cultures of Podophyllum hexandrum. Plant Cell Rep. 1990 Nov;9(7):382-5. doi: 10.1007/BF00232404. [PubMed:24227060 ]

Showing NP-Card for Podophyllotoxin 4-O-glucoside (NP0138526)

MOL for NP0138526 (Podophyllotoxin 4-O-glucoside)

3D MOL for NP0138526 (Podophyllotoxin 4-O-glucoside)

3D SDF for NP0138526 (Podophyllotoxin 4-O-glucoside)

3D-SDF for NP0138526 (Podophyllotoxin 4-O-glucoside)

PDB for NP0138526 (Podophyllotoxin 4-O-glucoside)

3D PDB for NP0138526 (Podophyllotoxin 4-O-glucoside)

SMILES for NP0138526 (Podophyllotoxin 4-O-glucoside)

INCHI for NP0138526 (Podophyllotoxin 4-O-glucoside)

Structure for NP0138526 (Podophyllotoxin 4-O-glucoside)

3D Structure for NP0138526 (Podophyllotoxin 4-O-glucoside)