4HLW

Targeting the Binding Function 3 (BF3) Site of the Human Androgen Receptor Through Virtual Screening. 2. Development of 2-((2-phenoxyethyl) thio)-1H-benzoimidazole derivatives.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Targeting the Binding Function 3 (BF3) Site of the Androgen Receptor Through Virtual Screening. 2. Development of 2-((2-phenoxyethyl) thio)-1H-benzimidazole Derivatives.

Munuganti, R.S.Leblanc, E.Axerio-Cilies, P.Labriere, C.Frewin, K.Singh, K.Hassona, M.D.Lack, N.A.Li, H.Ban, F.Tomlinson Guns, E.Young, R.Rennie, P.S.Cherkasov, A.

(2013) J Med Chem 56: 1136-1148

  • DOI: 10.1021/jm3015712
  • Primary Citation of Related Structures:  
    4HLW

  • PubMed Abstract: 
  • The human androgen receptor (AR) is a proven therapeutic target in prostate cancer. All current antiandrogens, such as Bicalutamide, Flutamide, Nilutamide, and Enzalutamide, target the buried hydrophobic androgen binding pocket of this protein. However, effective resistance mechanisms against these therapeutics exist such as mutations occurring at the target site ...

    The human androgen receptor (AR) is a proven therapeutic target in prostate cancer. All current antiandrogens, such as Bicalutamide, Flutamide, Nilutamide, and Enzalutamide, target the buried hydrophobic androgen binding pocket of this protein. However, effective resistance mechanisms against these therapeutics exist such as mutations occurring at the target site. To overcome these limitations, the surface pocket of the AR called binding function 3 (BF3) was characterized as an alternative target for small molecule therapeutics. A number of AR inhibitors directly targeting the BF3 were previously identified by us ( J. Med. Chem. 2011 . 54 , 8563 ). In the current study, based on the prior results, we have developed structure-activity relationships that allowed designing a series of 2-((2-phenoxyethyl)thio)-1H-benzimidazole and 2-((2-phenoxyethyl)thio)-1H-indole as lead BF3 inhibitors. Some of the developed BF3 ligands demonstrated significant antiandrogen potency against LNCaP and Enzalutamide-resistant prostate cancer cell lines.


    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Androgen receptorA256Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TES
Query on TES

Download Ideal Coordinates CCD File 
B [auth A]TESTOSTERONE
C19 H28 O2
MUMGGOZAMZWBJJ-DYKIIFRCSA-N
 Ligand Interaction
17W
Query on 17W

Download Ideal Coordinates CCD File 
C [auth A]2-[(2-phenoxyethyl)sulfanyl]-1H-benzimidazole
C15 H14 N2 O S
UEYUFQWEHMSHIX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TESKi:  1.399999976158142   nM  BindingDB
TESKi:  3.200000047683716   nM  BindingDB
TESIC50:  2.700000047683716   nM  BindingDB
TESIC50:  4.699999809265137   nM  BindingDB
TESIC50:  11   nM  BindingDB
TESIC50:  4.570000171661377   nM  BindingDB
17WIC50 :  4200   nM  PDBBind
TESIC50:  3090.300048828125   nM  BindingDB
TESIC50:  3.200000047683716   nM  BindingDB
TESIC50:  30   nM  BindingDB
TESKi:  29   nM  BindingDB
TESIC50:  4.199999809265137   nM  BindingDB
TESIC50:  6.5   nM  BindingDB
17WIC50:  21000   nM  BindingDB
TESEC50:  1.100000023841858   nM  BindingDB
TESKi:  4.300000190734863   nM  BindingDB
17WIC50:  4200   nM  BindingDB
17WIC50:  4300   nM  BindingDB
TESIC50:  4.300000190734863   nM  BindingDB
TESIC50:  3.9000000953674316   nM  BindingDB
TESEC50:  3.1600000858306885   nM  BindingDB
TESKi:  4.900000095367432   nM  BindingDB
TESEC50:  2   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.19α = 90
b = 66.3β = 90
c = 73.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references