NP-MRD: Showing NP-Card for (1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one (NP0212306)

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Record Information

Version

2.0

Created at

2022-09-05 10:55:54 UTC

Updated at

2022-09-05 10:55:54 UTC

NP-MRD ID

NP0212306

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one

Description

Xestokerol B belongs to the class of organic compounds known as cholesterols and derivatives. Cholesterols and derivatives are compounds containing a 3-hydroxylated cholestane core. (1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one was first documented in 2003 (PMID: 12808239). Based on a literature review very few articles have been published on Xestokerol B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052212552D          

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M  END

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M  END


  Mrv1652309052212552D          

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  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8  5  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  6  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 11 17  1  0  0  0  0
  8 17  1  0  0  0  0
 17 18  1  6  0  0  0
 13 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 26 25  1  6  0  0  0
 19 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 12 28  1  0  0  0  0
 28 29  1  1  0  0  0
  2 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0212306

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CCC(C)(O)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@H]4CC(=O)CC[C@]4(C)[C@H]3C[C@@H](O)[C@]12C)C1CC1C

> <INCHI_IDENTIFIER>
InChI=1S/C29H48O4/c1-16(20-12-17(20)2)8-11-28(4,33)24-7-6-21-26-22(15-25(32)29(21,24)5)27(3)10-9-19(30)13-18(27)14-23(26)31/h16-18,20-26,31-33H,6-15H2,1-5H3/t16?,17?,18-,20?,21+,22+,23-,24-,25-,26+,27+,28?,29+/m1/s1

> <INCHI_KEY>
UAWXUTQLQAYKSX-GVHFUGMBSA-N

> <FORMULA>
C29H48O4

> <MOLECULAR_WEIGHT>
460.699

> <EXACT_MASS>
460.355260026

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
55.48818109533918

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,7S,9R,10R,11S,14S,15S,16R)-9,16-dihydroxy-14-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-one

> <JCHEM_LOGP>
3.9814985146666677

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.032975582500086

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.420274724553963

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5822205340068586

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
130.82349999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,7S,9R,10R,11S,14S,15S,16R)-9,16-dihydroxy-14-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      12.717  -5.127   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.298  -3.701   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.353  -2.485   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.827  -2.696   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.882  -1.480   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.666  -2.425   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.098  -0.535   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.937  -0.264   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.365   1.215   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.090   2.079   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.874   1.134   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.358   1.405   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.366   0.228   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.889  -1.221   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.405  -1.492   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.928  -2.940   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       7.398  -0.314   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.069  -1.700   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.850   0.499   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.373  -0.949   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.857  -0.678   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.341  -0.407   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.182   1.041   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.698   1.312   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.810   2.218   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.326   1.947   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.319   3.125   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.835   2.854   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.828   4.031   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      14.823  -3.490   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      16.039  -2.545   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      16.250  -4.071   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      17.195  -5.287   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   30                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   17                                                  
CONECT   12   11   13   28                                                  
CONECT   13   12   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   11    8   18                                             
CONECT   18   17                                                            
CONECT   19   13   20   21   26                                             
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   19   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   12   29                                                  
CONECT   29   28                                                            
CONECT   30    2   31   32                                                  
CONECT   31   30   32                                                       
CONECT   32   31   30   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₈O₄

Average Mass

460.6990 Da

Monoisotopic Mass

460.35526 Da

IUPAC Name

(1S,2S,7S,9R,10R,11S,14S,15S,16R)-9,16-dihydroxy-14-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-one

Traditional Name

(1S,2S,7S,9R,10R,11S,14S,15S,16R)-9,16-dihydroxy-14-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-one

CAS Registry Number

Not Available

SMILES

CC(CCC(C)(O)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@H]4CC(=O)CC[C@]4(C)[C@H]3C[C@@H](O)[C@]12C)C1CC1C

InChI Identifier

InChI=1S/C29H48O4/c1-16(20-12-17(20)2)8-11-28(4,33)24-7-6-21-26-22(15-25(32)29(21,24)5)27(3)10-9-19(30)13-18(27)14-23(26)31/h16-18,20-26,31-33H,6-15H2,1-5H3/t16?,17?,18-,20?,21+,22+,23-,24-,25-,26+,27+,28?,29+/m1/s1

InChI Key

UAWXUTQLQAYKSX-GVHFUGMBSA-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

Not Available

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
20-hydroxysteroid
3-oxosteroid
12-hydroxysteroid
3-oxo-5-alpha-steroid
7-hydroxysteroid
Hydroxysteroid
Oxosteroid
Cyclic alcohol
Tertiary alcohol
Ketone
Cyclic ketone
Secondary alcohol
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Carbonyl group
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	3.98	ChemAxon
pKa (Strongest Acidic)	14.42	ChemAxon
pKa (Strongest Basic)	-0.58	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	130.82 m³·mol⁻¹	ChemAxon
Polarizability	55.49 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

24692214

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44584466

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Mitome H, Shinohara M, Miyaoka H, Yamada Y: Synthesis and anti-tumor activity of new steroidal nuclear analogues of aragusterol A. Chem Pharm Bull (Tokyo). 2003 Jun;51(6):640-5. doi: 10.1248/cpb.51.640. [PubMed:12808239 ]
LOTUS database [Link]

Showing NP-Card for (1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one (NP0212306)

MOL for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

3D MOL for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

3D SDF for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

3D-SDF for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

PDB for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

3D PDB for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

SMILES for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

INCHI for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

Structure for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)

3D Structure for NP0212306 ((1s,3as,3br,4r,5as,9as,9bs,11r,11as)-4,11-dihydroxy-1-[2-hydroxy-5-(2-methylcyclopropyl)hexan-2-yl]-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-7-one)