NP-MRD: Showing NP-Card for (1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol (NP0276879)

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Record Information

Version

2.0

Created at

2022-09-09 01:13:05 UTC

Updated at

2022-09-09 01:13:05 UTC

NP-MRD ID

NP0276879

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol

Description

Anhydroscymnol belongs to the class of organic compounds known as cholesterols and derivatives. Cholesterols and derivatives are compounds containing a 3-hydroxylated cholestane core. (1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol is found in Rhizoprionodon acutus. (1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol was first documented in 1991 (PMID: 1814607). Based on a literature review very few articles have been published on Anhydroscymnol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092203132D          

 32 36  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309092203132D          

 32 36  0  0  1  0            999 V2000
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  9 10  1  0  0  0  0
 11  2  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 15 14  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 14 20  1  0  0  0  0
 11 20  1  0  0  0  0
 20 21  1  6  0  0  0
 16 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  1  0  0  0
 26 28  1  0  0  0  0
 29 28  1  1  0  0  0
 22 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 15 31  1  0  0  0  0
 31 32  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0276879

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC[C@H]1OCC1CO)[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/C27H46O5/c1-15(4-7-23-16(13-28)14-32-23)19-5-6-20-25-21(12-24(31)27(19,20)3)26(2)9-8-18(29)10-17(26)11-22(25)30/h15-25,28-31H,4-14H2,1-3H3/t15-,16?,17+,18-,19-,20+,21+,22-,23-,24+,25+,26+,27-/m1/s1

> <INCHI_KEY>
PRQADQZRIHRYCH-OOQSZNCVSA-N

> <FORMULA>
C27H46O5

> <MOLECULAR_WEIGHT>
450.66

> <EXACT_MASS>
450.334524581

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
53.29006409386362

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5R,7S,9R,10R,11S,14R,15R,16S)-14-[(2R)-4-[(2R)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

> <JCHEM_LOGP>
2.2611100680000007

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.2963399055959

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.316725110831207

> <JCHEM_PKA_STRONGEST_BASIC>
-0.1593904195347865

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
124.3547

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5R,7S,9R,10R,11S,14R,15R,16S)-14-[(2R)-4-[(2R)-3-(hydroxymethyl)oxetan-2-yl]butan-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                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       9.302  -2.907   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.882  -1.480   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.407  -1.269   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.353  -2.485   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.878  -2.275   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      14.808  -1.047   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      16.036  -1.977   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.106  -3.204   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.316  -4.730   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      16.743  -5.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.937  -0.264   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.365   1.215   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.090   2.079   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.874   1.134   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.358   1.405   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.366   0.228   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.889  -1.221   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.405  -1.492   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.928  -2.940   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       7.398  -0.314   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.069  -1.700   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.850   0.499   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.373  -0.949   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.857  -0.678   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.341  -0.407   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.182   1.041   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -1.698   1.312   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.810   2.218   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.326   1.947   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.319   3.125   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.835   2.854   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.828   4.031   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    5    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    2   12   20                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15   14   16   31                                                  
CONECT   16   15   17   22                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   14   11   21                                             
CONECT   21   20                                                            
CONECT   22   16   23   24   29                                             
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   22   30                                                  
CONECT   30   29   31                                                       
CONECT   31   30   15   32                                                  
CONECT   32   31                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   72    0
END

View in JSmol

Synonyms

Value	Source
24,26-Epoxy-5 beta-cholestane-3 alpha,7 alpha,12 alpha,27-tetrol	MeSH

Chemical Formula

C₂₇H₄₆O₅

Average Mass

450.6600 Da

Monoisotopic Mass

450.33452 Da

IUPAC Name

(1S,2S,5R,7S,9R,10R,11S,14R,15R,16S)-14-[(2R)-4-[(2R)-3-(hydroxymethyl)oxetan-2-yl]butan-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)-4-[(2R)-3-(hydroxymethyl)oxetan-2-yl]butan-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]1OCC1CO)[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/C27H46O5/c1-15(4-7-23-16(13-28)14-32-23)19-5-6-20-25-21(12-24(31)27(19,20)3)26(2)9-8-18(29)10-17(26)11-22(25)30/h15-25,28-31H,4-14H2,1-3H3/t15-,16?,17+,18-,19-,20+,21+,22-,23-,24+,25+,26+,27-/m1/s1

InChI Key

PRQADQZRIHRYCH-OOQSZNCVSA-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 cholesterols and derivatives. Cholesterols and derivatives are compounds containing a 3-hydroxylated cholestane core.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Cholestane steroids

Direct Parent

Cholesterols and derivatives

Alternative Parents

Substituents

Cholesterol-skeleton
26-hydroxysteroid
7-hydroxysteroid
3-alpha-hydroxysteroid
Hydroxysteroid
12-hydroxysteroid
3-hydroxysteroid
Cyclic alcohol
Secondary alcohol
Oxetane
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

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	2.26	ChemAxon
pKa (Strongest Acidic)	15.32	ChemAxon
pKa (Strongest Basic)	-0.16	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	124.35 m³·mol⁻¹	ChemAxon
Polarizability	53.29 Å³	ChemAxon
Number of Rings	5	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

4955768

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6453386

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ishida H, Kinoshita S, Natsuyama R, Nukaya H, Tsuji K, Kosuge T, Yamaguchi K: Study on the bile salt, sodium scymnol sulfate, from Rhizoprionodon acutus. II. The structures of scymnol, anhydroscymnol and sodium scymnol sulfate. Chem Pharm Bull (Tokyo). 1991 Dec;39(12):3153-6. doi: 10.1248/cpb.39.3153. [PubMed:1814607 ]
LOTUS database [Link]

Showing NP-Card for (1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol (NP0276879)

MOL for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

3D MOL for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

3D SDF for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

3D-SDF for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

PDB for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

3D PDB for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

SMILES for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

INCHI for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

Structure for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)

3D Structure for NP0276879 ((1r,3as,3br,4r,5as,7r,9as,9bs,11s,11ar)-1-[(2r)-4-[(2r)-3-(hydroxymethyl)oxetan-2-yl]butan-2-yl]-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthrene-4,7,11-triol)