5CJ6

Crystal Structure of a Selective Androgen Receptor Modulator Bound to the Ligand Binding Domain of the Human Androgen Receptor

• PDB DOI: https://doi.org/10.2210/pdb5CJ6/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-14 Released: 2016-01-06 
• Deposition Author(s): Luz, J.G., Saeed, A., Wang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.222 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

2-Chloro-4-[[(1R,2R)-2-hydroxy-2-methyl-cyclopentyl]amino]-3-methyl-benzonitrile: A Transdermal Selective Androgen Receptor Modulator (SARM) for Muscle Atrophy.

Saeed, A., Vaught, G.M., Gavardinas, K., Matthews, D., Green, J.E., Losada, P.G., Bullock, H.A., Calvert, N.A., Patel, N.J., Sweetana, S.A., Krishnan, V., Henck, J.W., Luz, J.G., Wang, Y., Jadhav, P.

(2016) J Med Chem 59: 750-755

• PubMed: 26683992 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01168
• Primary Citation of Related Structures:  
  5CJ6


• PubMed Abstract: 
  

  A transdermal SARM has a potential to have therapeutic benefit through anabolic activity in muscle while sparing undesired effects of benign prostate hyperplasia (BPH) and liver-mediated decrease in HDL-C. 2-Chloro-4-[(2-hydroxy-2-methyl-cyclopentyl)amino]-3-methyl-benzonitrile 6 showed the desired muscle and prostate effects in a preclinical ORX rat model. Compound 6 had minimal effect on HDL-C levels in cynomolgus monkeys and showed human cadaver skin permeability, thus making it an effective tool for proof-of-concept studies in a clinical setting.

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Organizational Affiliation: 

Lilly Research Laboratories, Eli Lilly and Company , Lilly Corporate Center, Indianapolis, Indiana 46285, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 34.06 kDa 
• Atom Count: 2,233 
• Modelled Residue Count: 254 
• Deposited Residue Count: 293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Androgen receptor	A	283	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
small peptide	B	10	synthetic construct	Mutation(s): 0
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
51Y	C [auth A]	2-chloro-4-{[(1R,2R)-2-hydroxy-2-methylcyclopentyl]amino}-3-methylbenzonitrile C14 H17 Cl N2 O CXFSVKGROITHRY-TZMCWYRMSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
51Y	BindingDB:  5CJ6	Ki: 2 (nM) from 1 assay(s)
		EC50: 0.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.222 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.803	α = 90
b = 65.997	β = 90
c = 73.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-06 
Deposition Author(s): Luz, J.G., Saeed, A., Wang, Y.

Revision History  

• Version 1.0: 2016-01-06
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Database references
• Version 1.2: 2016-02-10
  Changes: Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations