Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.89 kDa 
• Atom Count: 2353 
• Modelled Residue Count: 245 
• Deposited Residue Count: 266 
• Unique protein chains: 1

2PNU

Crystal structure of human androgen receptor ligand-binding domain in complex with EM-5744

• DOI: 10.2210/pdb2PNU/pdb

• Classification: HORMONE/GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-04-25 Released: 2007-09-11 
• Deposition Author(s): Cantin, L., Faucher, F., Couture, J.F., Pereira de Jesus-Tran, K., Legrand, P., Ciobanu, C.L., Singh, S.M., Labrie, F., Breton, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.205 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 

Literature

Structural Characterization of the Human Androgen Receptor Ligand-binding Domain Complexed with EM5744, a Rationally Designed Steroidal Ligand Bearing a Bulky Chain Directed toward Helix 12.

Cantin, L., Faucher, F., Couture, J.F., de Jesus-Tran, K.P., Legrand, P., Ciobanu, L.C., Frechette, Y., Labrecque, R., Singh, S.M., Labrie, F., Breton, R.

(2007) J Biol Chem 282: 30910-30919

• PubMed: 17711855 
• DOI: 10.1074/jbc.M705524200
• Primary Citation of Related Structures:  
  2PNU


• PubMed Abstract: 
  

Antiandrogens are commonly used to treat androgen-dependent disorders. The currently used drugs unfortunately possess very weak affinity for the human AR (hAR), thus indicating the need to develop new high-affinity steroidal antiandrogens. Our compounds are specially designed to impede repositioning of the mobile carboxyl-terminal helix 12, which blocks the ligand-dependent transactivation function (AF-2) located in the AR ligand-binding domain (ARLBD). Using crystal structures of the hARLBD, we first found that H12 could be directly reached from the ligand-binding pocket (LBP) by a chain positioned on the C18 atom of an androgen steroid nucleus. A set of 5alpha-dihydrotestosterone-derived molecules bearing various C18 chains were thus synthesized and tested for their capacity to bind hAR and act as antagonists. Although most of those having very high affinity for hAR were agonists, several very potent antagonists were obtained, confirming the structural importance of the C18 chain. To understand the role of the C18 chain in their agonistic/antagonistic properties, the structure of the hARLBD complexed with one of these agonists, EM5744, was determined at a 1.65-A resolution. We have identified new interactions involving Gln(738), Met(742), and His(874) that explain both the high affinity of this compound and the inability of its bulky chain to prevent the repositioning of H12. This structural information will be helpful to refine the structure of the chains placed on the C18 atom to obtain efficient H12-directed steroidal antiandrogens.

---

Organizational Affiliation: 

Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUL) and Laval University, Québec G1V 4G2, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Androgen receptor	A	266	Homo sapiens	Mutation(s): 0  Gene Names: AR, DHTR, NR3C4
Find proteins for P10275 (Homo sapiens) Explore P10275  Go to UniProtKB:  P10275
NIH Common Fund Data Resources
PHAROS:  P10275 GTEx:  ENSG00000169083

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ENM	C [auth A]	(5S,8R,9S,10S,13R,14S,17S)-13-{2-[(3,5-DIFLUOROBENZYL)OXY]ETHYL}-17-HYDROXY-10-METHYLHEXADECAHYDRO-3H-CYCLOPENTA[A]PHENANTHREN-3-ONE C27 H36 F2 O3 AJODXHGZHBERGJ-JLYQOUBASA-N
MES	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
DTT	D [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.205 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.65	α = 90
b = 66.36	β = 90
c = 70.78	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data processing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-25 
• Released Date: 2007-09-11 
Deposition Author(s): Cantin, L., Faucher, F., Couture, J.F., Pereira de Jesus-Tran, K., Legrand, P., Ciobanu, C.L., Singh, S.M., Labrie, F., Breton, R.

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance