3RLJ | pdb_00003rlj

Crystal structure of the androgen receptor ligand binding domain in complex with SARM S-22

• PDB DOI: https://doi.org/10.2210/pdb3RLJ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-19 Released: 2011-05-04 
• Deposition Author(s): Bohl, C.E., Duke, C.B., Jones, A., Dalton, J.T., Miller, D.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.265 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Unexpected binding orientation of bulky-B-ring anti-androgens and implications for future drug targets.

Duke, C.B., Jones, A., Bohl, C.E., Dalton, J.T., Miller, D.D.

(2011) J Med Chem 54: 3973-3976

• PubMed: 21506597 
• DOI: https://doi.org/10.1021/jm2000097
• Primary Citation Related Structures: 
  3RLJ, 3RLL


• PubMed Abstract: 
  

  Several new androgen receptor antagonists were synthesized and found to have varying activities across typically anti-androgen resistant mutants (Thr877 → Ala and Trp741 → Leu) and markedly improved potency over previously reported pan-antagonists. X-ray crystallography of a new anti-androgen in an androgen receptor mutant (Thr877 → Ala) shows that the receptor can accommodate the added bulk presented by phenyl to naphthyl substitution, casting doubt on previous reports of predicted binding orientation and the causes of antagonism in bulky-B-ring antagonists.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, The University of Tennessee, Memphis, TN 38163, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.21 kDa 
• Atom Count: 2,225 
• Modeled Residue Count: 247 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Androgen receptor	A	247	Homo sapiens	Mutation(s): 0  Gene Names: AR, DHTR, NR3C4
UniProt & NIH Common Fund Data Resources
Find proteins for P10275 (Homo sapiens) Explore P10275  Go to UniProtKB:  P10275
PHAROS:  P10275 GTEx:  ENSG00000169083

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RLJ	B [auth A]	(2S)-3-(4-cyanophenoxy)-N-[4-cyano-3-(trifluoromethyl)phenyl]-2-hydroxy-2-methylpropanamide C19 H14 F3 N3 O3 JNGVJMBLXIUVRD-SFHVURJKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RLJ	BindingDB:  3RLJ	IC50: 36 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.265 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.742	α = 90
b = 66.795	β = 90
c = 69.374	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Bohl, C.E., Duke, C.B., Jones, A., Dalton, J.T., Miller, D.D.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description