Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.49 kDa 
• Atom Count: 2,108 
• Modelled Residue Count: 249 
• Deposited Residue Count: 258 
• Unique protein chains: 1

 5T8J

Synthesis and biological evaluation of novel selective androgen receptor modulators (SARMs). Part II: Optimization of 4-(pyrrolidin-1-yl)benzonitrile derivatives

• PDB DOI:  https://doi.org/10.2210/pdb5T8J/pdb

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


• Deposited: 2016-09-07 Released: 2017-04-26 
• Deposition Author(s): Wilson, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.305 
• R-Value Work: 0.197 
• R-Value Observed: 0.202 

Literature

Synthesis and biological evaluation of novel selective androgen receptor modulators (SARMs). Part II: Optimization of 4-(pyrrolidin-1-yl)benzonitrile derivatives.

Asano, M., Hitaka, T., Imada, T., Yamada, M., Morimoto, M., Shinohara, H., Hara, T., Yamaoka, M., Santou, T., Nakayama, M., Imai, Y., Habuka, N., Yano, J., Wilson, K., Fujita, H., Hasuoka, A.

(2017) Bioorg Med Chem Lett 27: 1897-1901

• PubMed: 28363748 
• DOI: https://doi.org/10.1016/j.bmcl.2017.03.038
• Primary Citation of Related Structures:  
  5T8E, 5T8J


• PubMed Abstract: 
  

We recently reported a class of novel tissue-selective androgen receptor modulators (SARMs), represented by a naphthalene derivative A. However, their pharmacokinetic (PK) profiles were poor due to low metabolic stability. To improve the PK profiles, we modified the hydroxypyrrolidine and benzonitrile substituents of 4-(pyrrolidin-1-yl)benzonitrile derivative B, which had a comparable potency as that of compound A. This optimization led us to further modifications, which improved metabolic stability while maintaining potent androgen agonistic activity. Among the synthesized compounds, (2S,3S)-2,3-dimethyl-3-hydroxylpyrrolidine derivative 1c exhibited a suitable PK profile and improved metabolic stability. Compound 1c demonstrated significant efficacy in levator ani muscle without increasing the weight of the prostate in an in vivo study. In addition, compound 1c showed agonistic activity in the CNS, which was detected using sexual behavior induction assay.

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Organizational Affiliation: 

Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Androgen receptor	A	258	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
77T	C [auth A]	2-fluoro-4-[(2S,3S)-3-hydroxy-2,3-dimethylpyrrolidin-1-yl]-3-methylbenzonitrile C14 H17 F N2 O OAXYYUPBCKQHBM-HZMBPMFUSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
77T	BindingDB:  5T8J	IC50: min: 0.29, max: 1 (nM) from 2 assay(s)
		EC50: 0.29 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.305 
• R-Value Work: 0.197 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.449	α = 90
b = 65.675	β = 90
c = 70.713	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Wilson, K.P.

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release