1EXA

ENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF THE HUMAN RETINOIC ACID RECEPTOR HRARGAMMA LIGAND BINDING DOMAIN: THE COMPLEX WITH THE ACTIVE R-ENANTIOMER BMS270394.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRARgamma.

Klaholz, B.P.Mitschler, A.Belema, M.Zusi, C.Moras, D.

(2000) Proc.Natl.Acad.Sci.USA 97: 6322-6327

  • Primary Citation of Related Structures:  1EXX

  • PubMed Abstract: 
  • The human retinoic acid receptor (hRAR) is a member of the nuclear receptor superfamily that regulates the transcription of target genes in a ligand-dependent manner. The three hRAR isotypes are targets for retinoids that are used in the treatment of ...

    The human retinoic acid receptor (hRAR) is a member of the nuclear receptor superfamily that regulates the transcription of target genes in a ligand-dependent manner. The three hRAR isotypes are targets for retinoids that are used in the treatment of various diseases, including breast cancer and skin diseases. Drug efficiency and safety depend on the pharmacological activity of enantiomers, which can differ because of the chiral environment generated by the target. We report the crystal structures of the hRARgamma ligand-binding domain bound to two enantiomers, the active BMS270394 and the inactive BMS270395, solved at 1.6 A and 1.7 A resolution, respectively. The crystal structures reveal that in both enantiomers, the hydroxyl moiety attached to the chiral center forms a hydrogen bond to the Met-272 sulfur atom, thus imposing a conformation of BMS270395 that differs significantly from that observed for BMS270394 and other known retinoids. BMS270395 adopts an energetically unfavorable conformation, accounting for its inactivity; in contrast, the conformation of BMS270394 is close to an energy minimum. Our high-resolution data allow rationalization of enantiomer discrimination by the receptor and provide a model system for the pharmacological properties of enantiomeric pairs.


    Related Citations: 
    • Conformational adaptation of agonists to the human nuclear receptor hRARgamma.
      Klaholz, B.P.,Renaud, J.-P.,Mitschler, A.,Zusi, C.,Chambon, P.,Gronemeyer, H.,Moras, D.
      (1998) Nat.Struct.Mol.Biol. 5: 199
    • Structural basis for isotype selectivity of the human retinoic acid nuclear receptor.
      Klaholz, B.P.,Mitschler, A.,Moras, D.
      (2000) TO BE PUBLISHED --: --


    Organizational Affiliation

    Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RETINOIC ACID RECEPTOR GAMMA-2
A
246Homo sapiensGene Names: RARG (NR1B3)
Find proteins for P13631 (Homo sapiens)
Go to Gene View: RARG
Go to UniProtKB:  P13631
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
394
Query on 394

Download SDF File 
Download CCD File 
A
R-3-FLUORO-4-[2-HYDROXY-2-(5,5,8,8-TETRAMETHYL-5,6,7,8,-TETRAHYDRO-NAPHTALEN-2-YL)-ACETYLAMINO]-BENZOIC ACID
BMS270394
C23 H26 F N O4
AANFHDFOMFRLLR-LJQANCHMSA-N
 Ligand Interaction
LMU
Query on LMU

Download SDF File 
Download CCD File 
A
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
394Ki: 1.5 nM (100) BINDINGDB
394Kd: 528 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.672α = 90.00
b = 59.672β = 90.00
c = 155.545γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance