NP-MRD: Showing NP-Card for (3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one (NP0332638)

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Record Information

Version

2.0

Created at

2024-03-14 02:53:53 UTC

Updated at

2024-11-01 00:38:01 UTC

NP-MRD ID

NP0332638

Natural Product DOI

https://doi.org/10.57994/1898

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one

Description

(3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one belongs to the class of organic compounds known as dihydroxy bile acids, alcohols and derivatives. Dihydroxy bile acids, alcohols and derivatives are compounds containing or derived from a bile acid or alcohol, and which bears exactly two carboxylic acid groups. Based on a literature review very few articles have been published on (3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03142402532D          

 29 32  0  0  1  0            999 V2000
    4.3228    1.7357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9629    0.9934    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4311    1.6241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6190    1.4789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6826    0.2174    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3340   -0.2889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0168    0.1741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7875    0.9666    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5977    0.8111    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2939    1.6179    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9830    2.3821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1111    1.5050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6175    2.1564    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1508    0.8481    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8705    0.0722    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4023   -0.5585    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387    0.7029    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0584   -0.0730    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5266    0.5577    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8069    1.3336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2463   -0.2182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342   -0.3634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0976    0.2673    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9098    0.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1827    1.0432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9948    1.1884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7781   -0.8489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5902   -0.7037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1220   -1.3344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  1  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  5 14  1  6  0  0  0
  5 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17  4  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 23 22  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 19 26  1  0  0  0  0
 21 27  2  0  0  0  0
 27 28  1  0  0  0  0
 15 28  1  0  0  0  0
 28 29  2  0  0  0  0
M  END


  Mrv2104 03142402532D          

 29 32  0  0  1  0            999 V2000
    4.3228    1.7357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9629    0.9934    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4311    1.6241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6190    1.4789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6826    0.2174    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3340   -0.2889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0168    0.1741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7875    0.9666    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5977    0.8111    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2939    1.6179    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9830    2.3821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1111    1.5050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6175    2.1564    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1508    0.8481    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8705    0.0722    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4023   -0.5585    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387    0.7029    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0584   -0.0730    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5266    0.5577    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8069    1.3336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2463   -0.2182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342   -0.3634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0976    0.2673    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9098    0.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1827    1.0432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9948    1.1884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7781   -0.8489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5902   -0.7037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1220   -1.3344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  1  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  5 14  1  6  0  0  0
  5 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17  4  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 23 22  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 19 26  1  0  0  0  0
 21 27  2  0  0  0  0
 27 28  1  0  0  0  0
 15 28  1  0  0  0  0
 28 29  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332638

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CC[C@@]2([H])[C@]3([H])C(=O)C=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CO

> <INCHI_IDENTIFIER>
InChI=1S/C22H34O3/c1-13(12-23)16-4-5-17-20-18(7-9-22(16,17)3)21(2)8-6-15(24)10-14(21)11-19(20)25/h11,13,15-18,20,23-24H,4-10,12H2,1-3H3/t13-,15+,16-,17+,18+,20+,21+,22-/m1/s1

> <INCHI_KEY>
BWJCSGDSKJURPU-IKLPAXEJSA-N

> <FORMULA>
C22H34O3

> <MOLECULAR_WEIGHT>
346.511

> <EXACT_MASS>
346.250794955

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
41.15250315769369

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,3aS,3bS,7S,9aR,9bS,11aR)-7-hydroxy-1-[(2S)-1-hydroxypropan-2-yl]-9a,11a-dimethyl-1H,2H,3H,3aH,3bH,4H,6H,7H,8H,9H,9aH,9bH,10H,11H,11aH-cyclopenta[a]phenanthren-4-one

> <JCHEM_LOGP>
3.1253649906666654

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.70620808145124

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.493524864380174

> <JCHEM_PKA_STRONGEST_BASIC>
-1.1732424923158091

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
100.15959999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3aS,3bS,7S,9aR,9bS,11aR)-7-hydroxy-1-[(2S)-1-hydroxypropan-2-yl]-9a,11a-dimethyl-1H,2H,3H,3aH,3bH,6H,7H,8H,9H,9bH,10H,11H-cyclopenta[a]phenanthren-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAR-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAR-24         0                                  
HETATM    1  C   UNK     0       8.069   3.240   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.398   1.854   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.405   3.032   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.889   2.761   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.874   0.406   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.090  -0.539   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.365   0.325   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.937   1.804   0.000  0.00  0.00           C+0
HETATM    9  H   UNK     0      10.449   1.514   0.000  0.00  0.00           H+0
HETATM   10  C   UNK     0       9.882   3.020   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.302   4.447   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.407   2.809   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      12.353   4.025   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       5.882   1.583   0.000  0.00  0.00           H+0
HETATM   15  C   UNK     0       5.358   0.135   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0       6.351  -1.043   0.000  0.00  0.00           H+0
HETATM   17  C   UNK     0       4.366   1.312   0.000  0.00  0.00           C+0
HETATM   18  H   UNK     0       3.842  -0.136   0.000  0.00  0.00           H+0
HETATM   19  C   UNK     0       2.850   1.041   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.373   2.489   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.326  -0.407   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.810  -0.678   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.182   0.499   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.698   0.228   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.341   1.947   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.857   2.218   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.319  -1.585   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.835  -1.314   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.828  -2.491   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5    8                                             
CONECT    3    2    4                                                       
CONECT    4    3   17                                                       
CONECT    5    2    6   14   15                                             
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    2    9   10                                             
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12                                                            
CONECT   14    5                                                            
CONECT   15    5   16   17   28                                             
CONECT   16   15                                                            
CONECT   17   15    4   18   19                                             
CONECT   18   17                                                            
CONECT   19   17   20   21   26                                             
CONECT   20   19                                                            
CONECT   21   19   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   19                                                       
CONECT   27   21   28                                                       
CONECT   28   27   15   29                                                  
CONECT   29   28                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₃₄O₃

Average Mass

346.5110 Da

Monoisotopic Mass

346.25079 Da

IUPAC Name

(1R,3aS,3bS,7S,9aR,9bS,11aR)-7-hydroxy-1-[(2S)-1-hydroxypropan-2-yl]-9a,11a-dimethyl-1H,2H,3H,3aH,3bH,4H,6H,7H,8H,9H,9aH,9bH,10H,11H,11aH-cyclopenta[a]phenanthren-4-one

Traditional Name

(1R,3aS,3bS,7S,9aR,9bS,11aR)-7-hydroxy-1-[(2S)-1-hydroxypropan-2-yl]-9a,11a-dimethyl-1H,2H,3H,3aH,3bH,6H,7H,8H,9H,9bH,10H,11H-cyclopenta[a]phenanthren-4-one

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC[C@@]2([H])[C@]3([H])C(=O)C=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CO

InChI Identifier

InChI=1S/C22H34O3/c1-13(12-23)16-4-5-17-20-18(7-9-22(16,17)3)21(2)8-6-15(24)10-14(21)11-19(20)25/h11,13,15-18,20,23-24H,4-10,12H2,1-3H3/t13-,15+,16-,17+,18+,20+,21+,22-/m1/s1

InChI Key

BWJCSGDSKJURPU-IKLPAXEJSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Kanazawa University	Kyoko Nakagawa-Goto	2024-03-14	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Kanazawa University	Kyoko Nakagawa-Goto	2024-03-14	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Kanazawa University	Kyoko Nakagawa-Goto	2024-03-14	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Kanazawa University	Kyoko Nakagawa-Goto	2024-03-14	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Kanazawa University	Kyoko Nakagawa-Goto	2024-03-14	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Kanazawa University	Kyoko Nakagawa-Goto	2024-03-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Kanazawa University	Kyoko Nakagawa-Goto	2024-03-14	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
delphinensis		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as dihydroxy bile acids, alcohols and derivatives. These are compounds containing or derived from a bile acid or alcohol, and which bears exactly two carboxylic acid 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

Dihydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Dihydroxy bile acid, alcohol, or derivatives
21-hydroxysteroid
Diterpenoid
7-oxosteroid
3-beta-hydroxysteroid
3-beta-hydroxy-delta-5-steroid
Oxosteroid
Hydroxysteroid
3-hydroxysteroid
3-hydroxy-delta-5-steroid
Delta-5-steroid
Long chain fatty alcohol
Fatty alcohol
Cyclohexenone
Fatty acyl
Alpha,beta-unsaturated ketone
Enone
Cyclic alcohol
Acryloyl-group
Secondary alcohol
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
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	3.13	ChemAxon
pKa (Strongest Acidic)	17.49	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	100.16 m³·mol⁻¹	ChemAxon
Polarizability	41.15 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

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Showing NP-Card for (3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one (NP0332638)

MOL for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

3D MOL for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

3D SDF for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

3D-SDF for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

PDB for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

3D PDB for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

SMILES for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

INCHI for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

Structure for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)

3D Structure for NP0332638 ((3S,8S,9S,10R,13R,14S,17R, 20S*)-3,21-dihydroxy-20-methylpregn-5-en-7-one)