NP-MRD: Showing NP-Card for (1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol (NP0328350)

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Record Information

Version

1.0

Created at

2022-09-12 11:44:48 UTC

Updated at

2022-09-12 11:44:48 UTC

NP-MRD ID

NP0328350

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol

Description

Tokorogenin belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Thus, tokorogenin is considered to be a sterol. (1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol is found in Dioscorea nipponica and Dioscorea tokoro. It was first documented in 2020 (PMID: 32378303). Based on a literature review a significant number of articles have been published on Tokorogenin (PMID: 36130844) (PMID: 36130843) (PMID: 36130842) (PMID: 36130841).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122213442D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309122213442D          

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 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 10 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
  7 20  1  0  0  0  0
 20 21  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
  6 23  1  0  0  0  0
  3 23  1  0  0  0  0
 23 24  1  1  0  0  0
  4 25  1  1  0  0  0
 26 25  1  1  0  0  0
  2 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
 26 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0328350

> <DATABASE_NAME>
NP-MRD

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

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

> <FORMULA>
C27H44O5

> <MOLECULAR_WEIGHT>
448.644

> <EXACT_MASS>
448.318874517

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
52.52401456792187

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'S,14'S,15'R,16'S,18'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]-14',15',16'-triol

> <JCHEM_LOGP>
3.3389851813333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.355906232536693

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.05056326105517

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1852563159591707

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
121.9849

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'S,14'S,15'R,16'S,18'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]-14',15',16'-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-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  C   UNK     0      21.880  -4.347   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.418  -4.258   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.264  -5.545   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      25.801  -5.455   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      23.573  -6.921   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      24.419  -8.208   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      22.035  -7.010   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      21.344  -8.386   0.000  0.00  0.00           O+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                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   10   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

Not Available

Chemical Formula

C₂₇H₄₄O₅

Average Mass

448.6440 Da

Monoisotopic Mass

448.31887 Da

IUPAC Name

(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'S,14'S,15'R,16'S,18'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]-14',15',16'-triol

Traditional Name

(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'S,14'S,15'R,16'S,18'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]-14',15',16'-triol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

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

SRTGQBIWSBCVSM-RXWDRLOESA-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
Dioscorea nipponica	LOTUS Database	35616633
Dioscorea tokoro	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
1-hydroxysteroid
2-hydroxysteroid
Hydroxysteroid
3-alpha-hydroxysteroid
Steroid
Ketal
Cyclitol or derivatives
Oxane
Cyclic alcohol
Tetrahydrofuran
Secondary alcohol
Acetal
Organoheterocyclic compound
Oxacycle
Polyol
Organooxygen compound
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Spirostanols and derivatives (LMST01080027 )

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	3.34	ChemAxon
pKa (Strongest Acidic)	13.05	ChemAxon
pKa (Strongest Basic)	-3.2	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	121.98 m³·mol⁻¹	ChemAxon
Polarizability	52.52 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

Not Available

Chemspider ID

20148244

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

20841762

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Cani I, Righini M, Cenni P, Foschi M: Teaching NeuroImage: Partially Reversible Widespread Leukoencephalopathy Associated With Atypical Hemolytic Uremic Syndrome. Neurology. 2022 Sep 21. pii: WNL.0000000000201378. doi: 10.1212/WNL.0000000000201378. [PubMed:36130844 ]
Sasaki R, Morimoto S, Ozawa F, Okano H, Yoshida M, Ishiura H, Tsuji S, Kuzuhara S, Kokubo Y: APOE Alleles With Tau and Abeta Pathology In Patients With Amyotrophic Lateral Sclerosis and Parkinsonism-Dementia Complex in the Kii Peninsula. Neurology. 2022 Sep 21. pii: WNL.0000000000201156. doi: 10.1212/WNL.0000000000201156. [PubMed:36130843 ]
Zhang Z, Wang M, Gill D, Liu X: Genetically Predicted Smoking and Alcohol Consumption and Functional Outcome After Ischemic Stroke. Neurology. 2022 Sep 21. pii: WNL.0000000000201291. doi: 10.1212/WNL.0000000000201291. [PubMed:36130842 ]
Khamis S, Mitakidou MR, Champion M, Goyal S, Jones RL, Siddiqui A, Sabanathan S, Hedderly T, Lin JP, Jungbluth H, Papandreou A: Clinical Reasoning: A Teenage Girl With Progressive Hyperkinetic Movements, Seizures, and Encephalopathy. Neurology. 2022 Sep 21. pii: WNL.0000000000201385. doi: 10.1212/WNL.0000000000201385. [PubMed:36130841 ]
Ukiya M, Sato D, Kimura H, Hirai Y, Nishina A: Tokoronin Contained in Dioscorea tokoro Makino ex Miyabe Suppressed alpha-MSH-Induced Melanogenesis in B16 Cells via Suppression of Classical MAPK Pathway Activation. Chem Biodivers. 2020 Jun;17(6):e2000077. doi: 10.1002/cbdv.202000077. Epub 2020 May 7. [PubMed:32378303 ]
LOTUS database [Link]

Showing NP-Card for (1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol (NP0328350)

MOL for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

3D MOL for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

3D SDF for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

3D-SDF for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

PDB for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

3D PDB for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

SMILES for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

INCHI for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

Structure for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)

3D Structure for NP0328350 ((1's,2r,2's,4's,5r,7's,8'r,9's,12's,13's,14's,15'r,16's,18'r)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane]-14',15',16'-triol)