1FD0

ISOTYPE SELECTIVITY OF THE HUMAN RETINOIC ACID NUCLEAR RECEPTOR HRAR: THE COMPLEX WITH THE RARGAMMA-SELECTIVE RETINOID SR11254


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

C-H...O hydrogen bonds in the nuclear receptor RARgamma--a potential tool for drug selectivity.

Klaholz, B.Moras, D.

(2002) Structure 10: 1197-1204

  • DOI: 10.1016/s0969-2126(02)00828-6
  • Primary Citation of Related Structures:  
    1FD0

  • PubMed Abstract: 
  • Hydrogen bonds between polarized atoms play a crucial role in protein interactions and are often used in drug design, which usually neglects the potential of C-H...O hydrogen bonds. The 1.4 A resolution crystal structure of the ligand binding domain ...

    Hydrogen bonds between polarized atoms play a crucial role in protein interactions and are often used in drug design, which usually neglects the potential of C-H...O hydrogen bonds. The 1.4 A resolution crystal structure of the ligand binding domain of the retinoic acid receptor RARgamma complexed with the retinoid SR11254 reveals several types of C-H...O hydrogen bonds. A striking example is the hydroxyl group of the ligand that acts as an H bond donor and acceptor, leading to a synergy between classical and C-H...O hydrogen bonds. This interaction introduces both specificity and affinity within the hydrophobic ligand pocket. The similarity of intraprotein and protein-ligand C-H...O interactions suggests that such bonds should be considered in rational drug design approaches.


    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., 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, BP 163, F-67404 Illkirch Cédex, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOIC ACID RECEPTOR GAMMA-1A235Homo 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
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  • 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
254
Query on 254

Download CCD File 
A
6-[HYDROXYIMINO-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-NAPHTALEN-2-YL)-METHYL]-NAPHTALENE-2-CARBOXYLIC ACID
C26 H27 N O3
RNZIUDLOJHVHLZ-SLEBQGDGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
254Kd :  4   nM  PDBBind
254Kd:  4   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.789α = 90
b = 59.789β = 90
c = 155.688γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-27
    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