4N8R

Crystal structure of RXRa LBD complexed with a synthetic modulator K-8008


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Sulindac-Derived RXR alpha Modulators Inhibit Cancer Cell Growth by Binding to a Novel Site.

Chen, L.Wang, Z.G.Aleshin, A.E.Chen, F.Chen, J.Jiang, F.Alitongbieke, G.Zeng, Z.Ma, Y.Huang, M.Zhou, H.Cadwell, G.Zheng, J.F.Huang, P.Q.Liddington, R.C.Zhang, X.K.Su, Y.

(2014) Chem.Biol. 21: 596-607

  • DOI: 10.1016/j.chembiol.2014.02.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Retinoid X receptor-alpha (RXRα), an intriguing and unique drug target, can serve as an intracellular target mediating the anticancer effects of certain nonsteroidal anti-inflammatory drugs (NSAIDs), including sulindac. We report the synthesis and ch ...

    Retinoid X receptor-alpha (RXRα), an intriguing and unique drug target, can serve as an intracellular target mediating the anticancer effects of certain nonsteroidal anti-inflammatory drugs (NSAIDs), including sulindac. We report the synthesis and characterization of two sulindac analogs, K-8008 and K-8012, which exert improved anticancer activities over sulindac in a RXRα-dependent manner. The analogs inhibit the interaction of the N-terminally truncated RXRα (tRXRα) with the p85α subunit of PI3K, leading to suppression of AKT activation and induction of apoptosis. Crystal structures of the RXRα ligand-binding domain (LBD) with K-8008 or K-8012 reveal that both compounds bind to tetrameric RXRα LBD at a site different from the classical ligand-binding pocket. Thus, these results identify K-8008 and K-8012 as tRXRα modulators and define a binding mechanism for regulating the nongenomic action of tRXRα.


    Organizational Affiliation

    School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China; Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: xzhang@sanfordburnham.org.,Department of Chemistry and Fujian Provincial Key Laboratory of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.,School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.,School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China; Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: ysu@sanfordburnham.org.,Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.,School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China; Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A, B, C, D
244Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K08
Query on K08

Download SDF File 
Download CCD File 
A, D
5-(2-{(1Z)-2-methyl-1-[4-(propan-2-yl)benzylidene]-1H-inden-3-yl}ethyl)-1H-tetrazole
C23 H24 N4
QSWFMFNUTKAURC-HMAPJEAMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K08IC50: 16800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.038α = 90.00
b = 99.347β = 98.68
c = 93.971γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-06-11
    Type: Database references