5C4O

Identification of a Novel Allosteric Binding Site for RORgt Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of an allosteric binding site for ROR gamma t inhibition.

Scheepstra, M.Leysen, S.van Almen, G.C.Miller, J.R.Piesvaux, J.Kutilek, V.van Eenennaam, H.Zhang, H.Barr, K.Nagpal, S.Soisson, S.M.Kornienko, M.Wiley, K.Elsen, N.Sharma, S.Correll, C.C.Trotter, B.W.van der Stelt, M.Oubrie, A.Ottmann, C.Parthasarathy, G.Brunsveld, L.

(2015) Nat Commun 6: 8833-8833

  • DOI: 10.1038/ncomms9833
  • Primary Citation of Related Structures:  4YPQ, 5C4S, 5C4T, 5C4U

  • PubMed Abstract: 
  • RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand ...

    RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand binding domain (LBD) of RORγt with a series of small-molecule antagonists demonstrates occupancy of a previously unreported allosteric binding pocket. Binding at this non-canonical site induces an unprecedented conformational reorientation of helix 12 in the RORγt LBD, which blocks cofactor binding. The functional consequence of this allosteric ligand-mediated conformation is inhibition of function as evidenced by both biochemical and cellular studies. RORγt function is thus antagonized in a manner molecularly distinct from that of previously described orthosteric RORγt ligands. This brings forward an approach to target RORγt for the treatment of Th17-mediated autoimmune diseases. The elucidation of an unprecedented modality of pharmacological antagonism establishes a mechanism for modulation of nuclear receptors.


    Organizational Affiliation

    Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute of Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600MB, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor ROR-gamma
A
241Homo sapiensGene Names: RORC (NR1F3, RORG, RZRG)
Find proteins for P51449 (Homo sapiens)
Go to Gene View: RORC
Go to UniProtKB:  P51449
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4F1
Query on 4F1

Download SDF File 
Download CCD File 
A
4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-1H-indazol-3-yl}benzoic acid
C22 H12 Cl F3 N2 O3
DANLZOIRUUHIIX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.490α = 90.00
b = 108.490β = 90.00
c = 104.660γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
PHASERphasing
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release