NP-MRD: Showing NP-Card for Gypsogenin (NP0052080)

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Record Information

Version

2.0

Created at

2022-04-27 23:15:10 UTC

Updated at

2022-04-27 23:15:10 UTC

NP-MRD ID

NP0052080

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gypsogenin

Description

Gypsogenin, also known as albsapogenin or astrantiagenin D, belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Thus, gypsogenin is considered to be an isoprenoid. Gypsogenin is found in Agrostemma githago, Chenopodium quinoa, Gypsophila bicolor, Gypsophila capillaris, Gypsophila oldhamiana, Gypsophila pacifica, Gypsophila spp., Luffa operculata , Medicago truncatula, Psammosilene tunicoides, Quillaja saponaria, Silene firma, Stellaria media and Swartzia spp.. Gypsogenin was first documented in 1998 (PMID: 9868165). Based on a literature review very few articles have been published on gypsogenin (PMID: 23561300).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282201152D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282201152D          

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  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  6  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
  7 14  1  6  0  0  0
 15 12  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 11 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 15 22  1  0  0  0  0
 21 23  1  0  0  0  0
 21 24  1  0  0  0  0
 16 25  1  6  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 11 28  1  1  0  0  0
  8 29  1  6  0  0  0
  5 30  1  6  0  0  0
  3 31  1  6  0  0  0
  3 32  1  1  0  0  0
 32 33  2  0  0  0  0
  2 34  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0052080

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@H](O)[C@@](C)(C=O)[C@@H]5CC[C@@]34C)[C@@H]2C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H46O4/c1-25(2)13-15-30(24(33)34)16-14-28(5)19(20(30)17-25)7-8-22-26(3)11-10-23(32)27(4,18-31)21(26)9-12-29(22,28)6/h7,18,20-23,32H,8-17H2,1-6H3,(H,33,34)/t20-,21+,22+,23-,26-,27-,28+,29+,30-/m0/s1

> <INCHI_KEY>
QMHCWDVPABYZMC-MYPRUECHSA-N

> <FORMULA>
C30H46O4

> <MOLECULAR_WEIGHT>
470.694

> <EXACT_MASS>
470.339609961

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
55.07727987614955

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4aS,6aS,6bR,8aR,9S,10S,12aR,12bR,14bS)-9-formyl-10-hydroxy-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid

> <ALOGPS_LOGP>
6.09

> <JCHEM_LOGP>
5.62790978

> <ALOGPS_LOGS>
-5.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.542738012599262

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.744259192511657

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9988063933192937

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
134.4163

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.44e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gypsogenin

> <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      11.344   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.114   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.344  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.804  -0.564   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.034   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.804   2.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.494  -1.897   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.034  -1.897   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.184   2.104   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.724   2.104   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.874  -1.897   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.414  -1.897   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.742   2.920   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.510   3.643   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.334  -1.897   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -0.206  -1.897   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       2.104  -3.231   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.954  -1.897   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.885  -2.095   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.264   2.104   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      12.650  -1.380   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.397  -2.103   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      12.757  -2.826   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      13.654   0.770   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   34                                                  
CONECT    3    2    4   31   32                                             
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   29                                             
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   18   28                                             
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13    7                                                       
CONECT   15   12   16   22                                                  
CONECT   16   15   17   19   25                                             
CONECT   17   16   18                                                       
CONECT   18   17   11                                                       
CONECT   19   16   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23   24                                             
CONECT   22   21   15                                                       
CONECT   23   21                                                            
CONECT   24   21                                                            
CONECT   25   16   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   11                                                            
CONECT   29    8                                                            
CONECT   30    5                                                            
CONECT   31    3                                                            
CONECT   32    3   33                                                       
CONECT   33   32                                                            
CONECT   34    2                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Value	Source
Albsapogenin	ChEBI
Astrantiagenin D	ChEBI
Githagenin	ChEBI
Gypsophilasapogenin	ChEBI
Gypsophilasaponin	ChEBI
Saponin-gypsophila	ChEBI

Chemical Formula

C₃₀H₄₆O₄

Average Mass

470.6940 Da

Monoisotopic Mass

470.33961 Da

IUPAC Name

(4aS,6aS,6bR,8aR,9S,10S,12aR,12bR,14bS)-9-formyl-10-hydroxy-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid

Traditional Name

gypsogenin

CAS Registry Number

Not Available

SMILES

CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@H](O)[C@@](C)(C=O)[C@@H]5CC[C@@]34C)[C@@H]2C1)C(O)=O

InChI Identifier

InChI=1S/C30H46O4/c1-25(2)13-15-30(24(33)34)16-14-28(5)19(20(30)17-25)7-8-22-26(3)11-10-23(32)27(4,18-31)21(26)9-12-29(22,28)6/h7,18,20-23,32H,8-17H2,1-6H3,(H,33,34)/t20-,21+,22+,23-,26-,27-,28+,29+,30-/m0/s1

InChI Key

QMHCWDVPABYZMC-MYPRUECHSA-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
Agrostemma githago	Plant	KNApSAcK
Chenopodium quinoa	LOTUS Database	35616633
Gypsophila bicolor	LOTUS Database	35616633
Gypsophila capillaris	LOTUS Database	35616633
Gypsophila oldhamiana	LOTUS Database	35616633
Gypsophila pacifica	Plant	KNApSAcK
Gypsophila spp.	Plant	KNApSAcK
Luffa operculata	Plant	KNApSAcK
Medicago truncatula	Plant	KNApSAcK
Psammosilene tunicoides	LOTUS Database	35616633
Quillaja saponaria	LOTUS Database	35616633
Silene firma	LOTUS Database	35616633
Stellaria media	LOTUS Database	35616633
Swartzia spp.	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
Steroid
Cyclic alcohol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aldehyde
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

monocarboxylic acid (CHEBI:5580 )
aldehyde (CHEBI:5580 )
pentacyclic triterpenoid (CHEBI:5580 )
sapogenin (CHEBI:5580 )
Oleanane triterpenoids (C08950 )
Ursanes (C08950 )
Oleanane triterpenoids (LMPR0106150010 )

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	6.09	ALOGPS
logP	5.63	ChemAxon
logS	-5.5	ALOGPS
pKa (Strongest Acidic)	4.74	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	134.42 m³·mol⁻¹	ChemAxon
Polarizability	55.08 Å³	ChemAxon
Number of Rings	5	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

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

92825

PDB ID

Not Available

ChEBI ID

5580

Good Scents ID

Not Available

References

General References

Voutquenne-Nazabadioko L, Gevrenova R, Borie N, Harakat D, Sayagh C, Weng A, Thakur M, Zaharieva M, Henry M: Triterpenoid saponins from the roots of Gypsophila trichotoma Wender. Phytochemistry. 2013 Jun;90:114-27. doi: 10.1016/j.phytochem.2013.03.001. Epub 2013 Apr 3. [PubMed:23561300 ]
Acebes B, Bernabe M, Diaz-Lanza AM, Bartolome C: Two new sulfated saponins from the roots of Gypsophila bermejoi. J Nat Prod. 1998 Dec;61(12):1557-9. doi: 10.1021/np9705221. [PubMed:9868165 ]

Showing NP-Card for Gypsogenin (NP0052080)

MOL for NP0052080 (Gypsogenin)

3D MOL for NP0052080 (Gypsogenin)

3D SDF for NP0052080 (Gypsogenin)

3D-SDF for NP0052080 (Gypsogenin)

PDB for NP0052080 (Gypsogenin)

3D PDB for NP0052080 (Gypsogenin)

SMILES for NP0052080 (Gypsogenin)

INCHI for NP0052080 (Gypsogenin)

Structure for NP0052080 (Gypsogenin)

3D Structure for NP0052080 (Gypsogenin)