2AM9

Crystal structure of human androgen receptor ligand binding domain in complex with testosterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparison of crystal structures of human androgen receptor ligand-binding domain complexed with various agonists reveals molecular determinants responsible for binding affinity.

Pereira de Jesus-Tran, K.Cote, P.-L.Cantin, L.Blanchet, J.Labrie, F.Breton, R.

(2006) Protein Sci. 15: 987-999

  • DOI: 10.1110/ps.051905906
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Androgens exert their effects by binding to the highly specific androgen receptor (AR). In addition to natural potent androgens, AR binds a variety of synthetic agonist or antagonist molecules with different affinities. To identify molecular determin ...

    Androgens exert their effects by binding to the highly specific androgen receptor (AR). In addition to natural potent androgens, AR binds a variety of synthetic agonist or antagonist molecules with different affinities. To identify molecular determinants responsible for this selectivity, we have determined the crystal structure of the human androgen receptor ligand-binding domain (hARLBD) in complex with two natural androgens, testosterone (Testo) and dihydrotestosterone (DHT), and with an androgenic steroid used in sport doping, tetrahydrogestrinone (THG), at 1.64, 1.90, and 1.75 A resolution, respectively. Comparison of these structures first highlights the flexibility of several residues buried in the ligand-binding pocket that can accommodate a variety of ligand structures. As expected, the ligand structure itself (dimension, presence, and position of unsaturated bonds that influence the geometry of the steroidal nucleus or the electronic properties of the neighboring atoms, etc.) determines the number of interactions it can make with the hARLBD. Indeed, THG--which possesses the highest affinity--establishes more van der Waals contacts with the receptor than the other steroids, whereas the geometry of the atoms forming electrostatic interactions at both extremities of the steroid nucleus seems mainly responsible for the higher affinity measured experimentally for DHT over Testo. Moreover, estimation of the ligand-receptor interaction energy through modeling confirms that even minor modifications in ligand structure have a great impact on the strength of these interactions. Our crystallographic data combined with those obtained by modeling will be helpful in the design of novel molecules with stronger affinity for the AR.


    Organizational Affiliation

    Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUL) and Laval University, Qu├ębec, QC G1V 4G2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Androgen receptor
A
266Homo sapiensMutation(s): 0 
Gene Names: AR (DHTR, NR3C4)
Find proteins for P10275 (Homo sapiens)
Go to Gene View: AR
Go to UniProtKB:  P10275
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

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Download CCD File 
A
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
TES
Query on TES

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Download CCD File 
A
TESTOSTERONE
C19 H28 O2
MUMGGOZAMZWBJJ-DYKIIFRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.820α = 90.00
b = 65.920β = 90.00
c = 71.040γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
PDB_EXTRACTdata extraction
XSCALEdata processing
CrystalCleardata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance