Crystal Structure of the Rat Androgen Receptor Ligand Binding Domain Complex with BMS-564929

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.249 

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Pharmacological and x-ray structural characterization of a novel selective androgen receptor modulator: potent hyperanabolic stimulation of skeletal muscle with hypostimulation of prostate in rats.

Ostrowski, J.Kuhns, J.E.Lupisella, J.A.Manfredi, M.C.Beehler, B.C.Krystek, S.R.Bi, Y.Sun, C.Seethala, R.Golla, R.Sleph, P.G.Fura, A.An, Y.Kish, K.F.Sack, J.S.Mookhtiar, K.A.Grover, G.J.Hamann, L.G.

(2007) Endocrinology 148: 4-12

  • DOI: https://doi.org/10.1210/en.2006-0843
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel, highly potent, orally active, nonsteroidal tissue selective androgen receptor (AR) modulator (BMS-564929) has been identified, and this compound has been advanced to clinical trials for the treatment of age-related functional decline. BMS-564929 is a subnanomolar AR agonist in vitro, is highly selective for the AR vs. other steroid hormone receptors, and exhibits no significant interactions with SHBG or aromatase. Dose response studies in castrated male rats show that BMS-564929 is substantially more potent than testosterone (T) in stimulating the growth of the levator ani muscle, and unlike T, highly selective for muscle vs. prostate. Key differences in the binding interactions of BMS-564929 with the AR relative to the native hormones were revealed through x-ray crystallography, including several unique contacts located in specific helices of the ligand binding domain important for coregulatory protein recruitment. Results from additional pharmacological studies effectively exclude alternative mechanistic contributions to the observed tissue selectivity of this unique, orally active androgen. Because concerns regarding the potential hyperstimulatory effects on prostate and an inconvenient route of administration are major drawbacks that limit the clinical use of T, the potent oral activity and tissue selectivity exhibited by BMS-564929 are expected to yield a clinical profile that provides the demonstrated beneficial effects of T in muscle and other tissues with a more favorable safety window.

  • Organizational Affiliation

    Department of Metabolic Diseases, Bristol-Myers Squibb, Pharmaceutical Research Institute, Princeton, NJ 08543, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Androgen receptor260Rattus norvegicusMutation(s): 0 
Gene Names: ArNr3c4
Find proteins for P15207 (Rattus norvegicus)
Explore P15207 
Go to UniProtKB:  P15207
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15207
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8NH

Download Ideal Coordinates CCD File 
C14 H12 Cl N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
8NH PDBBind:  2NW4 Ki: 2.11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.64α = 90
b = 65.62β = 90
c = 70.83γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description