Identification of a Novel Allosteric Binding Site for RORgt Inhibitors

Experimental Data Snapshot

  • Resolution: 1.77 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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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: https://doi.org/10.1038/ncomms9833
  • Primary Citation of Related Structures:  
    4YPQ, 5C4O, 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 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

    Merck Research Laboratories, 770 Sumneytown Pike, West Point, Pennsylvania 19486, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma241Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
GTEx:  ENSG00000143365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4Y6

Download Ideal Coordinates CCD File 
B [auth A](1S)-4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-4-fluoro-1H-indazol-3-yl}-1-methylcyclohex-3-ene-1-carboxylic acid
C23 H17 Cl F4 N2 O3
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
4Y6 BindingDB:  5C4T IC50: 21 (nM) from 1 assay(s)
Binding MOAD:  5C4T IC50: 21.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.77 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.27α = 90
b = 107.27β = 90
c = 100.39γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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