2NW4 | pdb_00002nw4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.293 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.218 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

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 Related Structures: 
    2NW4

  • 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.

Macromolecule Content 

  • Total Structure Weight: 30.59 kDa 
  • Atom Count: 2,031 
  • Modeled Residue Count: 248 
  • Deposited Residue Count: 260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Androgen receptor260Rattus norvegicusMutation(s): 0 
Gene Names: ArNr3c4
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8NH

Query on 8NH



Download:Ideal Coordinates CCD File
B [auth A]2-CHLORO-4-[(7R,7AS)-7-HYDROXY-1,3-DIOXOTETRAHYDRO-1H-PYRROLO[1,2-C]IMIDAZOL-2(3H)-YL]-3-METHYLBENZONITRILE
C14 H12 Cl N3 O3
KEJORAMIZFOODM-PWSUYJOCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.293 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.218 (DCC) 
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
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

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