Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 29.71 kDa 
• Atom Count: 2074 
• Modelled Residue Count: 249 
• Deposited Residue Count: 249 
• Unique protein chains: 1

2YHD

Human androgen receptor in complex with AF2 small molecule inhibitor

• PDB DOI: 10.2210/pdb2YHD/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-28 Released: 2011-09-21 
• Deposition Author(s): AxerioCilies, P., Lack, N.A., ShashiNayana, M.R., Chan, K.H., Yeung, A., LeBlanc, E., Guns, E., Rennie, P., Cherkasov, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.259 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Inhibitors of Androgen Receptor Activation Function-2 (Af2) Site Identified Through Virtual Screening.

Axerio-Cilies, P., Lack, N.A., Nayana, M.R., Chan, K.H., Yeung, A., Leblanc, E., Guns, E.S., Rennie, P.S., Cherkasov, A.

(2011) J Med Chem 54: 6197

• PubMed: 21846139 
• DOI: 10.1021/jm200532b
• Primary Citation of Related Structures:  
  2YHD


• PubMed Abstract: 
  

The androgen receptor (AR) is one of the most studied drug targets for the treatment of prostate cancer. However, all current anti-androgens directly interact with the AR at the androgen binding site, which is prone to resistant mutations, calling for new strategies of the AR inhibition. The current study represents the first attempt to use virtual screening to identify inhibitors of activation function-2 (AF2) of the human AR. By combining large-scale docking with experimental approaches, we were able to identify several small molecules that interact with the AF2 and effectively prevent the transcriptional activation of the AR. The crystallographic structure of one of these inhibitors in complex with the AR provides critical insight into the corresponding protein-ligand interactions and suitable for future hit optimization. Taken together, our results provide a promising ground for development of novel anti-androgens that can help to address the problem of drug resistance in prostate cancer.

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Organizational Affiliation: 

Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANDROGEN RECEPTOR	A	249	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TES	C [auth A]	TESTOSTERONE C19 H28 O2 MUMGGOZAMZWBJJ-DYKIIFRCSA-N
AV6	D [auth A]	4-(2,3-dihydro-1H-perimidin-2-yl)benzene-1,2-diol C17 H14 N2 O2 RBGFUFBYYJRGBW-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
TES	BindingDB:  2YHD	Ki: min: 1.4, max: 29 (nM) from 5 assay(s)
		IC50: min: 2.7, max: 3090.3 (nM) from 11 assay(s)
		EC50: min: 1.1, max: 3.16 (nM) from 3 assay(s)
AV6	PDBBind:  2YHD	Ki: 2.30e+4 (nM) from 1 assay(s)
	Binding MOAD:  2YHD	Ki: 2.30e+4 (nM) from 1 assay(s)
	BindingDB:  2YHD	IC50: min: 1.86e+4, max: 3.06e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.259 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.53	α = 90
b = 66.75	β = 90
c = 73.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
MOSFLM	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-28 
• Released Date: 2011-09-21 
Deposition Author(s): AxerioCilies, P., Lack, N.A., ShashiNayana, M.R., Chan, K.H., Yeung, A., LeBlanc, E., Guns, E., Rennie, P., Cherkasov, A.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references