Crystal structure of Androgen Receptor in complex with the ligand

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

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3-alkoxy-pyrrolo[1,2-b]pyrazolines as selective androgen receptor modulators with ideal physicochemical properties for transdermal administration

Ullrich, T.Sasmal, S.Boorgu, V.Pasagadi, S.Cheera, S.Rajagopalan, S.Bhumireddy, A.Shashikumar, D.Chelur, S.Belliappa, C.Pandit, C.Krishnamurthy, N.Mukherjee, S.Ramanathan, A.Ghadiyaram, C.Ramachandra, M.Santos, P.G.Lagu, B.Bock, M.G.Perrone, M.H.Weiler, S.Keller, H.

(2014) J Med Chem 57: 7396-7411

  • DOI: https://doi.org/10.1021/jm5009049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We describe the synthesis and characterization of 3-alkoxy-pyrrolo[1,2-b]pyrazolines as novel selective androgen receptor (AR) modulators that possess excellent physicochemical properties for transdermal administration. Compound 26 bound to human AR with an IC50 of 0.7 nM with great selectivity over other nuclear hormone receptors and potently activated AR in a C2C12 muscle cell reporter gene assay with an EC50 of 0.5 nM. It showed high aqueous solubility of 1.3 g/L at pH 7.4, and an in silico model as well as a customized parallel artificial membrane permeability assay indicated good skin permeation. Indeed, when measuring skin permeation through excised human skin, an excellent flux of 2 μg/(cm(2)·h) was determined without any permeation enhancers. In a 2 week Hershberger model using castrated rats, the compound showed dose-dependent effects fully restoring skeletal muscle weight at 0.3 mg/kg/day after subcutaneous administration with high selectivity over prostate stimulation.

  • Organizational Affiliation

    Global Discovery Chemistry and #Musculoskeletal Diseases, Novartis Institutes for BioMedical Research , CH-4002 Basel, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Androgen receptor259Homo sapiensMutation(s): 0 
Gene Names: ARDHTRNR3C4
UniProt & NIH Common Fund Data Resources
Find proteins for P10275 (Homo sapiens)
Explore P10275 
Go to UniProtKB:  P10275
PHAROS:  P10275
GTEx:  ENSG00000169083 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10275
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JAD

Download Ideal Coordinates CCD File 
B [auth A]2-chloro-4-[(3S,3aS,4S)-4-hydroxy-3-methoxy-3a,4,5,6-tetrahydro-3H-pyrrolo[1,2-b]pyrazol-2-yl]-3-methylbenzonitrile
C15 H16 Cl N3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
JAD BindingDB:  4QL8 IC50: 0.7 (nM) from 1 assay(s)
EC50: 0.5 (nM) from 1 assay(s)
Binding MOAD:  4QL8 IC50: 0.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.129α = 90
b = 65.476β = 90
c = 68.964γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description