NP-MRD: Showing NP-Card for agigenin (NP0195175)

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Record Information

Version

2.0

Created at

2022-09-04 12:58:54 UTC

Updated at

2022-09-04 12:58:54 UTC

NP-MRD ID

NP0195175

Secondary Accession Numbers

None

Natural Product Identification

Common Name

agigenin

Description

Agigenin belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Thus, agigenin is considered to be a sterol. agigenin is found in Allium ampeloprasum, Allium giganteum, Allium obliquum and Allium rotundum. agigenin was first documented in 1976 (PMID: 1028596). Based on a literature review a small amount of articles have been published on agigenin (PMID: 22513009) (PMID: 9358643).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042214582D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309042214582D          

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M  END
> <DATABASE_ID>
NP0195175

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4C[C@@H](O)[C@H]5C[C@@H](O)[C@H](O)C[C@]5(C)[C@H]4CC[C@]23C)O[C@]11CC[C@@H](C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C27H44O5/c1-14-5-8-27(31-13-14)15(2)24-23(32-27)11-18-16-9-20(28)19-10-21(29)22(30)12-26(19,4)17(16)6-7-25(18,24)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>
FYRLHXNMINIDCB-LEGLVIAUSA-N

> <FORMULA>
C27H44O5

> <MOLECULAR_WEIGHT>
448.644

> <EXACT_MASS>
448.318874517

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
52.83511199962027

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,15'R,16'R,18'S,19'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-15',16',19'-triol

> <JCHEM_LOGP>
2.949216531333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.817835866266197

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.853114690139979

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8343239602193195

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
122.3699

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,15'R,16'R,18'S,19'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-15',16',19'-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0      13.454  -7.989   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.686  -6.467   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.054  -5.760   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.805  -4.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.173  -3.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.268  -4.616   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.805  -4.526   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      19.497  -3.150   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.034  -3.061   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      21.725  -1.685   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      21.880  -4.347   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      23.418  -4.258   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.264  -5.545   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      25.801  -5.455   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      23.573  -6.921   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      24.419  -8.208   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      22.035  -7.010   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      21.189  -5.724   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      20.498  -7.100   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      19.652  -5.813   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      18.960  -7.189   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      17.423  -7.279   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      16.577  -5.992   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      15.746  -7.289   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      13.282  -4.008   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      12.591  -5.384   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.048  -6.825   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.528  -7.075   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.552  -5.884   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.032  -6.134   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.095  -4.443   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      11.615  -4.193   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4   23                                                  
CONECT    4    3    5   25                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   23                                                  
CONECT    7    6    8   20                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   11   19   20                                             
CONECT   19   18                                                            
CONECT   20   18    7   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22    6    3   24                                             
CONECT   24   23                                                            
CONECT   25    4   26                                                       
CONECT   26   25    2   27   32                                             
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   26                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   74    0
END

View in JSmol

Synonyms

Value	Source
(25R)-5alpha-Spirostan-2alpha,3beta,6beta-triol	MeSH

Chemical Formula

C₂₇H₄₄O₅

Average Mass

448.6440 Da

Monoisotopic Mass

448.31887 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4C[C@@H](O)[C@H]5C[C@@H](O)[C@H](O)C[C@]5(C)[C@H]4CC[C@]23C)O[C@]11CC[C@@H](C)CO1

InChI Identifier

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

FYRLHXNMINIDCB-LEGLVIAUSA-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
Allium ampeloprasum	LOTUS Database	35616633
Allium giganteum	LOTUS Database	35616633
Allium obliquum	LOTUS Database	35616633
Allium rotundum	LOTUS Database	35616633

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
6-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:72849 )
organic heterohexacyclic compound (CHEBI:72849 )
oxaspiro compound (CHEBI:72849 )
2alpha-hydroxy steroid (CHEBI:72849 )
Spirostanols and derivatives (LMST01080015 )

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

C00050327

Chemspider ID

23339606

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44566818

PDB ID

Not Available

ChEBI ID

72849

Good Scents ID

Not Available

References

General References

Lanzotti V, Barile E, Antignani V, Bonanomi G, Scala F: Antifungal saponins from bulbs of garlic, Allium sativum L. var. Voghiera. Phytochemistry. 2012 Jun;78:126-34. doi: 10.1016/j.phytochem.2012.03.009. Epub 2012 Apr 16. [PubMed:22513009 ]
Syrov VN, Kurmukov AG: [Experimental study of the anabolic activity of 6-ketoderivatives of certain natural sapogenins]. Farmakol Toksikol. 1976 Sep-Oct;39(5):631-5. [PubMed:1028596 ]
Carotenuto A, Fattorusso E, Lanzotti V, Magno S, De Feo V, Carnuccio R, D'Acquisto F: Porrigenins A and B, novel cytotoxic and antiproliferative sapogenins isolated from Allium porrum. J Nat Prod. 1997 Oct;60(10):1003-7. doi: 10.1021/np960657r. [PubMed:9358643 ]
LOTUS database [Link]

Showing NP-Card for agigenin (NP0195175)

MOL for NP0195175 (agigenin)

3D MOL for NP0195175 (agigenin)

3D SDF for NP0195175 (agigenin)

3D-SDF for NP0195175 (agigenin)

PDB for NP0195175 (agigenin)

3D PDB for NP0195175 (agigenin)

SMILES for NP0195175 (agigenin)

INCHI for NP0195175 (agigenin)

Structure for NP0195175 (agigenin)

3D Structure for NP0195175 (agigenin)