2AMA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.214 

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:  
    2AM9, 2AMB, 2AMA

  • 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, Québec, QC G1V 4G2, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Androgen receptorA266Homo sapiensMutation(s): 0 
Gene Names: ARDHTRNR3C4
Find proteins for P10275 (Homo sapiens)
Explore P10275 
Go to UniProtKB:  P10275
NIH Common Fund Data Resources
PHAROS  P10275
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHT
Query on DHT

Download Ideal Coordinates CCD File 
A
5-ALPHA-DIHYDROTESTOSTERONE
C19 H30 O2
NVKAWKQGWWIWPM-ABEVXSGRSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DHTKi:  0.30000001192092896   nM  BindingDB
DHTKi:  0.8999999761581421   nM  BindingDB
DHTKi:  10   nM  BindingDB
DHTEC50:  20   nM  BindingDB
DHTEC50:  5.099999904632568   nM  BindingDB
DHTEC50:  2   nM  BindingDB
DHTKi:  0.4300000071525574   nM  BindingDB
DHTEC50:  3   nM  BindingDB
DHTEC50:  0.18000000715255737   nM  BindingDB
DHTKi:  0.6899999976158142   nM  BindingDB
DHTKi:  2   nM  BindingDB
DHTEC50:  1   nM  BindingDB
DHTEC50:  0.9700000286102295   nM  BindingDB
DHTEC50:  6   nM  BindingDB
DHTEC50:  5   nM  BindingDB
DHTEC50:  0.05000000074505806   nM  BindingDB
DHTKi:  3   nM  BindingDB
DHTKi:  0.27000001072883606   nM  BindingDB
DHTIC50:  0   nM  BindingDB
DHTKi:  0.2800000011920929   nM  BindingDB
DHTKi:  0.20000000298023224   nM  BindingDB
DHTEC50:  5.699999809265137   nM  BindingDB
DHTIC50 :  10   nM  PDBBind
DHTEC50:  6.199999809265137   nM  BindingDB
DHTKi:  4.699999809265137   nM  BindingDB
DHTEC50:  2.799999952316284   nM  BindingDB
DHTEC50:  3.9800000190734863   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.5α = 90
b = 66.3β = 90
c = 70.7γ = 90
Software Package:
Software NamePurpose
XSCALEdata processing
CNSrefinement
PDB_EXTRACTdata extraction
XNEMOdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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