5ZQU

Crystal structure of tetrameric RXRalpha-LBD complexed with partial agonist CBt-PMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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Literature

Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor alpha (RXR alpha ).

Miyashita, Y.Numoto, N.Arulmozhiraja, S.Nakano, S.Matsuo, N.Shimizu, K.Shibahara, O.Fujihara, M.Kakuta, H.Ito, S.Ikura, T.Ito, N.Tokiwa, H.

(2019) FEBS Lett 593: 242-250

  • DOI: https://doi.org/10.1002/1873-3468.13301
  • Primary Citation of Related Structures:  
    5ZQU

  • PubMed Abstract: 

    1-[(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)amino]benzotriazole-5-carboxylic acid (CBt-PMN), a partial agonist of retinoid X receptor (RXR), has attracted attention due to its potential to treat type 2 diabetes and central nervous system diseases with reduced adverse effects of existing full agonists. Herein, we report the crystal structure of CBt-PMN-bound ligand-binding domain of human RXRα (hRXRα) and its biochemical characterization. Interestingly, the structure is a tetramer in nature, in which CBt-PMNs are clearly found binding in two different conformations. The dynamics of the hRXRα/CBt-PMN complex examined using molecular dynamics simulations suggest that the flexibility of the AF-2 interface depends on the conformation of the ligand. These facts reveal that the dual conformation of CBt-PMN in the complex is probably the reason behind its partial agonistic activity.


  • Organizational Affiliation

    Department of Chemistry, Rikkyo University, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha
A, B, C, D
243Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
GTEx:  ENSG00000186350 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9HF (Subject of Investigation/LOI)
Query on 9HF

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
O [auth C]
R [auth D]
E [auth A],
F [auth A],
K [auth B],
O [auth C],
R [auth D],
S [auth D]
1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic acid
C22 H25 N3 O2
QSRQAKVNYDAVIT-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
L [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
T [auth D],
U [auth D]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
9HF BindingDB:  5ZQU EC50: 143 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.571α = 90
b = 100.492β = 99.269
c = 111.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description