6A22

Ternary complex of Human ROR gamma Ligand Binding Domain With Compound T.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Ternary crystal structure of human ROR gamma ligand-binding-domain, an inhibitor and corepressor peptide provides a new insight into corepressor interaction

Noguchi, M.Nomura, A.Doi, S.Yamaguchi, K.Hirata, K.Shiozaki, M.Maeda, K.Hirashima, S.Kotoku, M.Yamaguchi, T.Katsuda, Y.Crowe, P.Tao, H.Thacher, S.Adachi, T.

(2018) Sci Rep 8: 17374-17374

  • DOI: 10.1038/s41598-018-35783-9

  • PubMed Abstract: 
  • Retinoic acid-related orphan receptor gamma (RORγ) plays pivotal roles in autoimmune diseases by controlling the lineage of interleukin 17 (IL-17)-producing CD4 <sup>+ </sup> T cells (Th17 cells). Structure-based drug design has proven fruitful in th ...

    Retinoic acid-related orphan receptor gamma (RORγ) plays pivotal roles in autoimmune diseases by controlling the lineage of interleukin 17 (IL-17)-producing CD4 + T cells (Th17 cells). Structure-based drug design has proven fruitful in the development of inhibitors targeting the ligand binding domain (LBD) of RORγ. Here, we present the crystal structure of a novel RORγ inhibitor co-complex, in the presence of a corepressor (CoR) peptide. This ternary complex with compound T reveals the structural basis for an inhibitory mechanism different from the previously reported inverse agonist. Compared to the inverse agonist, compound T induces about 2 Å shift of helix 5 (H5) backbone and side-chain conformational changes of Met365 on H5. These conformational changes correlate to reduced CoR peptide binding to RORγ-LBD in the presence of compound T, which suggests that the shift of H5 is responsible. This crystal structure analysis will provide useful information for the development of novel and efficacious drugs for autoimmune disorders.


    Organizational Affiliation

    Orphagen Pharmaceuticals, 11558 Sorrento Valley Road, Suite 4, San Diego, California, 92121, USA.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan. tsuyoshi.adachi@jt.com.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan.,Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Biological Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan. masato.noguchi@jt.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor ROR-gamma
A, C, E, G
258Homo sapiensMutation(s): 2 
Gene Names: RORC (NR1F3, RORG, RZRG)
Find proteins for P51449 (Homo sapiens)
Go to Gene View: RORC
Go to UniProtKB:  P51449
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor corepressor 2
B, D, F, H
22Homo sapiensMutation(s): 0 
Gene Names: NCOR2 (CTG26)
Find proteins for Q9Y618 (Homo sapiens)
Go to Gene View: NCOR2
Go to UniProtKB:  Q9Y618
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9P6
Query on 9P6

Download SDF File 
Download CCD File 
A, C, E, G
2-[2-[1-~{tert}-butyl-5-(4-methoxyphenyl)pyrazol-4-yl]-1,3-thiazol-4-yl]-~{N}-(oxan-4-ylmethyl)ethanamide
C25 H32 N4 O3 S
SRKLUIJNVCRLFZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.926α = 90.00
b = 73.277β = 89.99
c = 100.204γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release