1FCY

ISOTYPE SELECTIVITY OF THE HUMAN RETINOIC ACID NUCLEAR RECEPTOR HRAR: THE COMPLEX WITH THE RARBETA/GAMMA-SELECTIVE RETINOID CD564


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for isotype selectivity of the human retinoic acid nuclear receptor.

Klaholz, B.P.Mitschler, A.Moras, D.

(2000) J Mol Biol 302: 155-170

  • DOI: 10.1006/jmbi.2000.4032
  • Primary Citation of Related Structures:  
    1FCZ, 1FCY, 1FCX

  • PubMed Abstract: 
  • The human retinoic acid receptor (hRAR) belongs to the family of nuclear receptors that regulate transcription in a ligand-dependent way. The isotypes RARalpha,beta and gamma are distinct pharmacological targets for retinoids that are involved in the ...

    The human retinoic acid receptor (hRAR) belongs to the family of nuclear receptors that regulate transcription in a ligand-dependent way. The isotypes RARalpha,beta and gamma are distinct pharmacological targets for retinoids that are involved in the treatment of various skin diseases and cancers, in particular breast cancer and acute promyelocytic leukemia. Therefore, synthetic retinoids have been developed aiming at isotype selectivity and reduced side-effects. We report the crystal structures of three complexes of the hRARgamma ligand-binding domain (LBD) bound to agonist retinoids that possess selectivity either for RARgamma (BMS184394) or for RARbeta/gamma (CD564), or that are potent for all RAR-isotypes (panagonist BMS181156). The high resolution data (1.3-1. 5 A) provide a description at the atomic level of the ligand pocket revealing the molecular determinants for the different degrees of ligand selectivity. The comparison of the complexes of the chemically closely related retinoids BMS184394 and CD564 shows that the side-chain of Met272 adopts different conformations depending on the presence of a hydrogen bond between its sulfur atom and the ligand. This accounts for their different isotype selectivity. On the other hand, the difference between the pan- and the RARbeta, gamma-selective agonist is probably due to a steric discrimination at the level of the 2-naphthoic acid moiety of CD564. Based on this study, we propose a model for a complex with the RARgamma-specific agonist CD666 that shows the possible applications for structure-based drug design of RAR isotype-selective retinoids.


    Related Citations: 
    • 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
    • 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
    • Crystal structure of the RARgamma ligand-binding domain bound to all-trans retinoic acid.
      Renaud, J.-P., Rochel, N., Ruff, M., Vivat, V., Chambon, P., Gronemeyer, H., Moras, D.
      (1995) Nature 378: 681

    Organizational Affiliation

    Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1, rue Laurent Fries, Illkirch Cédex, BP 163, F-67404, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOIC ACID RECEPTOR GAMMA-1A236Homo sapiensMutation(s): 0 
Gene Names: RARGNR1B3
Find proteins for P13631 (Homo sapiens)
Explore P13631 
Go to UniProtKB:  P13631
NIH Common Fund Data Resources
PHAROS  P13631
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMU
Query on LMU

Download CCD File 
A
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
564
Query on 564

Download CCD File 
A
6-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-NAPHTALENE-2-CARBONYL)-NAPHTALENE-2-CARBOXYLIC ACID
C26 H26 O3
RWYREGSYPCNZTL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
564Kd:  1.2000000476837158   nM  BindingDB
564Kd:  1.2000000476837158   nM  BindingDB
564Kd :  3   nM  PDBBind
564Kd:  3   nM  Binding MOAD
564Kd:  3   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.849α = 90
b = 59.849β = 90
c = 155.158γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-11
    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