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 

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Ligand Structure Quality Assessment 


This is version 1.3 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 U S A 97: 6322-6327

  • DOI: https://doi.org/10.1073/pnas.97.12.6322
  • Primary Citation of Related Structures:  
    1EXA, 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RETINOIC ACID RECEPTOR GAMMA-2246Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P13631 (Homo sapiens)
Explore P13631 
Go to UniProtKB:  P13631
GTEx:  ENSG00000172819 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13631
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMU
Query on LMU

Download Ideal Coordinates CCD File 
C [auth A]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
394
Query on 394

Download Ideal Coordinates CCD File 
B [auth A]R-3-FLUORO-4-[2-HYDROXY-2-(5,5,8,8-TETRAMETHYL-5,6,7,8,-TETRAHYDRO-NAPHTALEN-2-YL)-ACETYLAMINO]-BENZOIC ACID
C23 H26 F N O4
AANFHDFOMFRLLR-LJQANCHMSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
394 BindingDB:  1EXA Ki: 1.5 (nM) from 1 assay(s)
Kd: 528 (nM) from 1 assay(s)
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
b = 59.672β = 90
c = 155.545γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description