1XNN

CRYSTAL STRUCTURE OF THE RAT ANDROGEN RECEPTOR LIGAND BINDING DOMAIN T877A MUTANT COMPLEX WITH (3A-ALPHA-,4-ALPHA 7-ALPHA-,7A-ALPHA-)-3A,4,7,7A-TETRAHYDRO-2-(4-NITRO-1-NAPHTHALENYL)-4,7-ETHANO-1H-ISOINDOLE-1,3(2H)-DIONE.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.249 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Structure based approach to the design of bicyclic-1H-isoindole-1,3(2H)-dione based androgen receptor antagonists.

Salvati, M.E., Balog, A., Shan, W., Wei, D.D., Pickering, D., Attar, R.M., Geng, J., Rizzo, C.A., Gottardis, M.M., Weinmann, R., Krystek, S.R., Sack, J., An, Y., Kish, K.

(2005) Bioorg Med Chem Lett 15: 271-276

  • DOI: 10.1016/j.bmcl.2004.10.085
  • Primary Citation of Related Structures:  
    1XNN

  • PubMed Abstract: 

    • A novel series of isoindoledione based compounds were identified as potent antagonists of the androgen receptor (AR). Co-crystallization of members of this family of inhibitors was successfully accomplished with the T877A AR LBD. A working model of how this class of compounds functions to antagonize the AR was created ...

    A novel series of isoindoledione based compounds were identified as potent antagonists of the androgen receptor (AR). Co-crystallization of members of this family of inhibitors was successfully accomplished with the T877A AR LBD. A working model of how this class of compounds functions to antagonize the AR was created. Based on this model, it was proposed that expanding the bicyclic portion of the molecule should result in analogs which function as effective antagonists against a variety of AR isoforms. In contrast to what was predicted by the model, SAR around this new series was dictated by the aniline portion rather than the bicyclic portion of the molecule.

    Organizational Affiliation: 

    Department of Oncology Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, PO Box 4000, Princeton, NJ 08543-4000, USA. mark.salvati@bms.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Androgen receptorA260Rattus norvegicusMutation(s): 1 
Gene Names: Ar, Nr3c4
UniProt
Find proteins for P15207 (Rattus norvegicus)
Explore P15207 
Go to UniProtKB:  P15207
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15207
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HYQ
Query on HYQ
Download Ideal Coordinates CCD File 
B [auth A]REL-(3AR,4S,7R,7AS)-3A,4,7,7A-TETRAHYDRO-2-(4-NITRO-1-NAPHTHALENYL)-4,7-ETHANO-1H-ISOINDOLE-1,3(2H)-DIONE
C20 H18 N2 O4
DEJXHCDDTLTVNB-FRVJLOGJSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HYQ Binding MOAD:  1XNN Ki: 0.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.87α = 90
b = 65.94β = 90
c = 70.46γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2004-10-05 
  • Released Date: 2005-10-11 
    • Deposition Author(s): Sack, J.

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations