1EXX

ENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF THE HUMAN RETINOIC ACID RECEPTOR HRARGAMMA LIGAND BINDING DOMAIN: THE COMPLEX WITH THE INACTIVE S-ENANTIOMER BMS270395.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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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: 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 ...

    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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOIC ACID RECEPTOR GAMMA-2A246Homo sapiensMutation(s): 0 
Gene Names: RARGNR1B3
UniProt & NIH Common Fund Data Resources
Find proteins for P13631 (Homo sapiens)
Explore P13631 
Go to UniProtKB:  P13631
PHAROS:  P13631
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMU (Subject of Investigation/LOI)
Query on LMU

Download Ideal Coordinates CCD File 
C [auth A]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
961 (Subject of Investigation/LOI)
Query on 961

Download Ideal Coordinates CCD File 
B [auth A]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-IBGZPJMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.849α = 90
b = 59.849β = 90
c = 155.615γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
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: 2019-07-24
    Changes: Data collection, Refinement description