2YLO

TARGETING THE BINDING FUNCTION 3 SITE OF THE ANDROGEN RECEPTOR THROUGH IN SILICO MOLECULAR MODELING

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Targeting the Binding Function 3 (Bf3) Site of the Human Androgen Receptor Through Virtual Screening.

Lack, N.A., Axerio-Cilies, P., Tavassoli, P., Han, F.Q., Chan, K.H., Feau, C., Leblanc, E., Guns, E.T., Guy, R.K., Rennie, P.S., Cherkasov, A.

(2011) J Med Chem 54: 8563

  • DOI: 10.1021/jm201098n
  • Primary Citation of Related Structures:  
    2YLO, 2YLP, 2YLQ, 3ZQT

  • PubMed Abstract: 

    • The androgen receptor (AR) is the best studied drug target for the treatment of prostate cancer. While there are a number of drugs that target the AR, they all work through the same mechanism of action and are prone to the development of drug resistance. There is a large unmet need for novel AR inhibitors which work through alternative mechanism(s) ...

    The androgen receptor (AR) is the best studied drug target for the treatment of prostate cancer. While there are a number of drugs that target the AR, they all work through the same mechanism of action and are prone to the development of drug resistance. There is a large unmet need for novel AR inhibitors which work through alternative mechanism(s). Recent studies have identified a novel site on the AR called binding function 3 (BF3) that is involved into AR transcriptional activity. In order to identify inhibitors that target the BF3 site, we have conducted a large-scale in silico screen followed by experimental evaluation. A number of compounds were identified that effectively inhibited the AR transcriptional activity with no obvious cytotoxicity. The mechanism of action of these compounds was validated by biochemical assays and X-ray crystallography. These findings lay a foundation for the development of alternative or supplementary therapies capable of combating prostate cancer even in its antiandrogen resistant forms.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ANDROGEN RECEPTORA256Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10275
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YLO
Query on YLO
Download Ideal Coordinates CCD File 
D [auth A]1-[2-(4-METHYLPHENOXY)ETHYL]-2-(2-PHENOXYETHYLSULFANYL)BENZIMIDAZOLE
C24 H24 N2 O2 S
PNCBJXVNIRRHJP-UHFFFAOYSA-N		 Ligand Interaction
TES
Query on TES
Download Ideal Coordinates CCD File 
B [auth A]TESTOSTERONE
C19 H28 O2
MUMGGOZAMZWBJJ-DYKIIFRCSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TES BindingDB:  2YLO 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)
YLO BindingDB:  2YLO IC50: min: 1.00e+4, max: 5.00e+4 (nM) from 3 assay(s)
PDBBind:  2YLO IC50: 1.31e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.32α = 90
b = 66.5β = 90
c = 73.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references, Version format compliance
  • Version 1.2: 2012-01-11
    Changes: Other