NP-MRD: Showing NP-Card for scymnol (NP0142025)

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Record Information

Version

2.0

Created at

2022-09-01 20:28:32 UTC

Updated at

2022-09-01 20:28:32 UTC

NP-MRD ID

NP0142025

Secondary Accession Numbers

None

Natural Product Identification

Common Name

scymnol

Description

5Beta-scymnol, also known as scymnol, belongs to the class of organic compounds known as pentahydroxy bile acids, alcohols and derivatives. These are bile acids, alcohols or derivatives bearing five hydroxyl groups. Thus, 5beta-scymnol is considered to be a bile acid. scymnol is found in Rhizoprionodon acutus. scymnol was first documented in 2010 (PMID: 20038666). Based on a literature review a significant number of articles have been published on 5beta-scymnol (PMID: 33904732) (PMID: 30844411) (PMID: 27234873) (PMID: 21961050) (PMID: 20974163).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309012222282D          

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 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 15 21  1  0  0  0  0
 12 21  1  0  0  0  0
 21 22  1  6  0  0  0
 17 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
 30 29  1  1  0  0  0
 23 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 16 32  1  0  0  0  0
 32 33  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0142025

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC[C@@H](O)C(CO)CO)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C27H48O6/c1-15(4-7-22(31)16(13-28)14-29)19-5-6-20-25-21(12-24(33)27(19,20)3)26(2)9-8-18(30)10-17(26)11-23(25)32/h15-25,28-33H,4-14H2,1-3H3/t15-,17+,18-,19-,20+,21+,22-,23-,24+,25+,26+,27-/m1/s1

> <INCHI_KEY>
DIPHJTHZUWDJIK-JPLAUYQNSA-N

> <FORMULA>
C27H48O6

> <MOLECULAR_WEIGHT>
468.675

> <EXACT_MASS>
468.345089266

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
54.49206347267805

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5R,7S,9R,10R,11S,14R,15R,16S)-14-[(2R,5R)-5,7-dihydroxy-6-(hydroxymethyl)heptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

> <ALOGPS_LOGP>
1.67

> <JCHEM_LOGP>
1.0994064956666674

> <ALOGPS_LOGS>
-3.59

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.260580614254764

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.597647016133802

> <JCHEM_PKA_STRONGEST_BASIC>
-0.15943471521351016

> <JCHEM_POLAR_SURFACE_AREA>
121.38000000000001

> <JCHEM_REFRACTIVITY>
127.86479999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.21e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5R,7S,9R,10R,11S,14R,15R,16S)-14-[(2R,5R)-5,7-dihydroxy-6-(hydroxymethyl)heptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 01-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.193  -9.054   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.653  -9.054   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.883  -7.721   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.657  -7.721   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.427  -6.387   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.657  -5.053   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.967  -6.387   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.737  -5.053   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.277  -5.053   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.737  -7.721   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.277  -7.721   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.883 -10.388   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.509 -11.795   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.365 -12.825   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.969 -12.055   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.433 -12.531   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.578 -11.501   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.258  -9.994   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.793  -9.518   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.473  -8.012   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.649 -10.549   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.173  -9.084   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.042 -11.977   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.722 -10.470   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.187 -10.946   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.652 -11.422   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.972 -12.928   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       9.436 -13.404   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       6.827 -13.959   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.363 -13.483   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.218 -14.513   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.754 -14.038   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.609 -15.068   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    7   11                                                       
CONECT   11   10                                                            
CONECT   12    2   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   21                                                  
CONECT   16   15   17   32                                                  
CONECT   17   16   18   23                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   15   12   22                                             
CONECT   22   21                                                            
CONECT   23   17   24   25   30                                             
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   23   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   16   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

View in JSmol

Synonyms

Value	Source
5beta-Cholestane-3alpha,7alpha,12alpha,24,26,27-hexol	ChEBI
Scymnol	ChEBI
5b-Cholestane-3a,7a,12a,24,26,27-hexol	Generator
5Β-cholestane-3α,7α,12α,24,26,27-hexol	Generator
5b-Scymnol	Generator
5Β-scymnol	Generator
5 beta-Cholestane-3alpha,7 alpha,12 alpha,24,26,27-hexol	MeSH

Chemical Formula

C₂₇H₄₈O₆

Average Mass

468.6750 Da

Monoisotopic Mass

468.34509 Da

IUPAC Name

(1S,2S,5R,7S,9R,10R,11S,14R,15R,16S)-14-[(2R,5R)-5,7-dihydroxy-6-(hydroxymethyl)heptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

Traditional Name

(1S,2S,5R,7S,9R,10R,11S,14R,15R,16S)-14-[(2R,5R)-5,7-dihydroxy-6-(hydroxymethyl)heptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

CAS Registry Number

Not Available

SMILES

C[C@H](CC[C@@H](O)C(CO)CO)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C

InChI Identifier

InChI=1S/C27H48O6/c1-15(4-7-22(31)16(13-28)14-29)19-5-6-20-25-21(12-24(33)27(19,20)3)26(2)9-8-18(30)10-17(26)11-23(25)32/h15-25,28-33H,4-14H2,1-3H3/t15-,17+,18-,19-,20+,21+,22-,23-,24+,25+,26+,27-/m1/s1

InChI Key

DIPHJTHZUWDJIK-JPLAUYQNSA-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
Rhizoprionodon acutus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentahydroxy bile acids, alcohols and derivatives. These are bile acids, alcohols or derivatives bearing five hydroxyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Pentahydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Pentahydroxy bile acid, alcohol, or derivatives
26-hydroxysteroid
24-hydroxysteroid
3-hydroxysteroid
7-hydroxysteroid
3-alpha-hydroxysteroid
12-hydroxysteroid
Hydroxysteroid
Fatty alcohol
Fatty acyl
Cyclic alcohol
Secondary alcohol
Polyol
Primary alcohol
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

3alpha-hydroxy steroid (CHEBI:50106 )
7alpha-hydroxy steroid (CHEBI:50106 )
27-hydroxy steroid (CHEBI:50106 )
12alpha-hydroxy steroid (CHEBI:50106 )
26-hydroxy steroid (CHEBI:50106 )
24-hydroxy steroid (CHEBI:50106 )
C27 bile acids, alcohols, and derivatives (LMST04030173 )

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	1.67	ALOGPS
logP	1.1	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	14.6	ChemAxon
pKa (Strongest Basic)	-0.16	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	121.38 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	127.86 m³·mol⁻¹	ChemAxon
Polarizability	54.49 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

145073

KEGG Compound ID

C16260

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

5Beta-Scymnol

METLIN ID

Not Available

PubChem Compound

165531

PDB ID

Not Available

ChEBI ID

50106

Good Scents ID

Not Available

References

General References

Halkias C, Darby WG, Feltis BN, McIntyre P, Macrides TA, Wright PFA: Marine Bile Natural Products as Agonists of the TGR5 Receptor. J Nat Prod. 2021 May 28;84(5):1507-1514. doi: 10.1021/acs.jnatprod.0c01327. Epub 2021 Apr 27. [PubMed:33904732 ]
Glowacki LL, Hodges LD, Wynne PM, Wright PFA, Kalafatis N, Macrides TA: LC-MSMS characterisations of scymnol and oxoscymnol biotransformations in incubation mixtures of rat liver microsomes. Biochimie. 2019 May;160:130-140. doi: 10.1016/j.biochi.2019.02.016. Epub 2019 Mar 4. [PubMed:30844411 ]
Hodges LD, Carter F, Kalafatis N, Wright PF, Macrides TA: Elucidation of the hepatoprotective moiety of 5beta-scymnol that suppresses paracetamol toxicity in mice. Mol Cell Biochem. 2016 Jun;417(1-2):135-40. doi: 10.1007/s11010-016-2720-3. Epub 2016 May 27. [PubMed:27234873 ]
Muthusamy V, Hodges LD, Macrides TA, Boyle GM, Piva TJ: Effect of novel marine nutraceuticals on IL-1alpha-mediated TNF-alpha release from UVB-irradiated human melanocyte-derived cells. Oxid Med Cell Longev. 2011;2011:728645. doi: 10.1155/2011/728645. Epub 2011 Sep 22. [PubMed:21961050 ]
Glowacki LL, Hodges LD, Wynne PM, Kalafatis N, Wright PF, Macrides TA: Hydroxysteroid dehydrogenase transformations of 5beta-scymnol and identification of oxoscymnol transformation products by liquid chromatography-tandem mass spectroscopy. Steroids. 2011 Jan;76(1-2):163-8. doi: 10.1016/j.steroids.2010.10.007. Epub 2010 Oct 23. [PubMed:20974163 ]
Huertas M, Hagey L, Hofmann AF, Cerda J, Canario AV, Hubbard PC: Olfactory sensitivity to bile fluid and bile salts in the European eel (Anguilla anguilla), goldfish (Carassius auratus) and Mozambique tilapia (Oreochromis mossambicus) suggests a 'broad range' sensitivity not confined to those produced by conspecifics alone. J Exp Biol. 2010 Jan 15;213(2):308-17. doi: 10.1242/jeb.033142. [PubMed:20038666 ]
LOTUS database [Link]

Showing NP-Card for scymnol (NP0142025)

MOL for NP0142025 (scymnol)

3D MOL for NP0142025 (scymnol)

3D SDF for NP0142025 (scymnol)

3D-SDF for NP0142025 (scymnol)

PDB for NP0142025 (scymnol)

3D PDB for NP0142025 (scymnol)

SMILES for NP0142025 (scymnol)

INCHI for NP0142025 (scymnol)

Structure for NP0142025 (scymnol)

3D Structure for NP0142025 (scymnol)