NP-MRD: Showing NP-Card for Digitogenin (NP0052114)

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Record Information

Version

2.0

Created at

2022-04-27 23:17:07 UTC

Updated at

2022-04-27 23:17:08 UTC

NP-MRD ID

NP0052114

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Digitogenin

Description

Digitogenin, also known as digitonin aglycon, belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Thus, digitogenin is considered to be a sterol. Digitogenin is found in Digitalis lanata Ehrh. and Digitalis purpurea . Digitogenin was first documented in 1971 (PMID: 5545780). Based on a literature review a small amount of articles have been published on digitogenin (PMID: 17135046) (PMID: 6097588).

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652304282201172D          

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M  END

     RDKit          3D

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M  END

  Mrv1652304282201172D          

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M  END
> <DATABASE_ID>
NP0052114

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@@H](O[C@]11CC[C@@H](C)CO1)[C@@H](O)[C@H]1[C@@H]3CC[C@H]4C[C@@H](O)[C@H](O)C[C@]4(C)[C@H]3CC[C@]21C

> <INCHI_IDENTIFIER>
InChI=1S/C27H44O5/c1-14-7-10-27(31-13-14)15(2)21-24(32-27)23(30)22-17-6-5-16-11-19(28)20(29)12-26(16,4)18(17)8-9-25(21,22)3/h14-24,28-30H,5-13H2,1-4H3/t14-,15+,16+,17-,18+,19-,20-,21+,22-,23+,24-,25-,26+,27-/m1/s1

> <INCHI_KEY>
COVOPPXLDJVUSC-JPYPKGSXSA-N

> <FORMULA>
C27H44O5

> <MOLECULAR_WEIGHT>
448.644

> <EXACT_MASS>
448.318874517

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
53.12352699150364

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'R,2R,2'S,3'S,4'R,5R,7'S,8'R,9'S,12'S,13'S,15'R,16'R,18'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-3',15',16'-triol

> <ALOGPS_LOGP>
2.01

> <JCHEM_LOGP>
3.2610314513333343

> <ALOGPS_LOGS>
-4.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.188235704060787

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.60217577711207

> <JCHEM_PKA_STRONGEST_BASIC>
-3.148853305227826

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
122.0619

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.62e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1'R,2R,2'S,3'S,4'R,5R,7'S,8'R,9'S,12'S,13'S,15'R,16'R,18'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-3',15',16'-triol

> <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      13.158   9.072   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.849   7.696   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.003   6.409   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.465   6.499   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.774   7.875   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.620   9.161   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.237   7.964   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.390   6.678   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.082   5.301   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.619   5.212   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.853   6.767   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.162   8.143   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.008   9.430   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.545   9.340   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.639   7.911   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.390   6.391   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.758   5.684   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.990   4.162   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.867   6.159   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.176   7.536   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.271   8.618   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.039  10.141   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.200   6.344   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.320   6.594   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.863   8.035   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.113   9.226   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.632   8.976   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.383   8.285   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.330   9.440   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.083   9.251   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      15.386   7.606   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      14.004  10.359   0.000  0.00  0.00           O+0
CONECT    1    2    6   32                                                  
CONECT    2    1    3   31                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   30                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   17                                                  
CONECT   12   11   13   15   29                                             
CONECT   13   12   14                                                       
CONECT   14   13    7                                                       
CONECT   15   12   16   21                                                  
CONECT   16   15   17   19                                                  
CONECT   17   16   11   18                                                  
CONECT   18   17                                                            
CONECT   19   16   20                                                       
CONECT   20   19   21   23   27                                             
CONECT   21   20   15   22                                                  
CONECT   22   21                                                            
CONECT   23   20   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   28                                                  
CONECT   26   25   27                                                       
CONECT   27   26   20                                                       
CONECT   28   25                                                            
CONECT   29   12                                                            
CONECT   30    5                                                            
CONECT   31    2                                                            
CONECT   32    1                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   74    0
END

View in JSmol

Synonyms

Value	Source
Digitonin aglycon	ChEBI

Chemical Formula

C₂₇H₄₄O₅

Average Mass

448.6440 Da

Monoisotopic Mass

448.31887 Da

IUPAC Name

(1'R,2R,2'S,3'S,4'R,5R,7'S,8'R,9'S,12'S,13'S,15'R,16'R,18'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-3',15',16'-triol

Traditional Name

(1'R,2R,2'S,3'S,4'R,5R,7'S,8'R,9'S,12'S,13'S,15'R,16'R,18'S)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-3',15',16'-triol

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@@H](O[C@]11CC[C@@H](C)CO1)[C@@H](O)[C@H]1[C@@H]3CC[C@H]4C[C@@H](O)[C@H](O)C[C@]4(C)[C@H]3CC[C@]21C

InChI Identifier

InChI=1S/C27H44O5/c1-14-7-10-27(31-13-14)15(2)21-24(32-27)23(30)22-17-6-5-16-11-19(28)20(29)12-26(16,4)18(17)8-9-25(21,22)3/h14-24,28-30H,5-13H2,1-4H3/t14-,15+,16+,17-,18+,19-,20-,21+,22-,23+,24-,25-,26+,27-/m1/s1

InChI Key

COVOPPXLDJVUSC-JPYPKGSXSA-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
Digitalis lanata	Plant	KNApSAcK
Digitalis purpurea	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Spirostane skeleton
3-hydroxysteroid
2-hydroxysteroid
15-hydroxysteroid
Hydroxysteroid
3-beta-hydroxysteroid
Steroid
Ketal
Oxane
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Polyol
Acetal
Organoheterocyclic compound
Oxacycle
Organic oxygen compound
Organooxygen compound
Alcohol
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

3beta-hydroxy steroid (CHEBI:28431 )
2alpha-hydroxy steroid (CHEBI:28431 )
15beta-hydroxy steroid (CHEBI:28431 )
spirostan (C08896 )
Spirostanols and derivatives (C08896 )
Spirostan and derivatives (C08896 )
Spirostanols and derivatives (LMST01080004 )

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	2.01	ALOGPS
logP	3.26	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	13.6	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	79.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	122.06 m³·mol⁻¹	ChemAxon
Polarizability	53.12 Å³	ChemAxon
Number of Rings	6	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

C00003573

Chemspider ID

390462

KEGG Compound ID

C08896

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

441886

PDB ID

Not Available

ChEBI ID

28431

Good Scents ID

Not Available

References

General References

Zhang L, Xu LZ, Yang SL: Two new cardenolides from the roots of Streptocaulon griffithii. J Asian Nat Prod Res. 2006 Oct-Nov;8(7):613-7. doi: 10.1080/10286020500208519. [PubMed:17135046 ]
Cowley PS, Evans FJ, Ginman RF: A gas-liquid chromatographic determination of the ratio of gitogenin and digitogenin in mixtures. J Chromatogr. 1971 Jan 20;54(2):185-91. doi: 10.1016/s0021-9673(01)80264-8. [PubMed:5545780 ]
Nishikawa M, Nojima S, Akiyama T, Sankawa U, Inoue K: Interaction of digitonin and its analogs with membrane cholesterol. J Biochem. 1984 Oct;96(4):1231-9. doi: 10.1093/oxfordjournals.jbchem.a134941. [PubMed:6097588 ]

Showing NP-Card for Digitogenin (NP0052114)

MOL for NP0052114 (Digitogenin)

3D MOL for NP0052114 (Digitogenin)

3D SDF for NP0052114 (Digitogenin)

3D-SDF for NP0052114 (Digitogenin)

PDB for NP0052114 (Digitogenin)

3D PDB for NP0052114 (Digitogenin)

SMILES for NP0052114 (Digitogenin)

INCHI for NP0052114 (Digitogenin)

Structure for NP0052114 (Digitogenin)

3D Structure for NP0052114 (Digitogenin)