5X8X

Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ternary complex of human ROR gamma ligand-binding domain, inverse agonist and SMRT peptide shows a unique mechanism of corepressor recruitment

Noguchi, M.Nomura, A.Murase, K.Doi, S.Yamaguchi, K.Hirata, K.Shiozaki, M.Hirashima, S.Kotoku, M.Yamaguchi, T.Katsuda, Y.Steensma, R.Li, X.Tao, H.Tse, B.Fenn, M.Babine, R.Bradley, E.Crowe, P.Thacher, S.Adachi, T.Kamada, M.

(2017) Genes Cells 22: 535-551

  • DOI: 10.1111/gtc.12494
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Retinoid-related orphan receptor gamma (RORγ) directly controls the differentiation of Th17 cell and the production of interleukin-17, which plays an integral role in autoimmune diseases. To obtain insight into RORγ, we have determined the first crys ...

    Retinoid-related orphan receptor gamma (RORγ) directly controls the differentiation of Th17 cell and the production of interleukin-17, which plays an integral role in autoimmune diseases. To obtain insight into RORγ, we have determined the first crystal structure of a ternary complex containing RORγ ligand-binding domain (LBD) bound with a novel synthetic inhibitor and a repressor peptide, 22-mer peptide from silencing mediator of retinoic acid and thyroid hormone receptor (SMRT). Comparison of a binary complex of nonliganded (apo) RORγ-LBD with a nuclear receptor co-activator (NCoA-1) peptide has shown that our inhibitor displays a unique mechanism different from those caused by natural inhibitor, ursolic acid (UA). The compound unprecedentedly induces indirect disruption of a hydrogen bond between His479 on helix 11 (H11) and Tyr502 on H12, which is crucial for active conformation. This crystallographic study will allow us to develop novel synthetic compounds for autoimmune disease therapy.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, C, E, G
258Nomascus leucogenysMutation(s): 2 
Gene Names: RORC
Find proteins for G1RH57 (Nomascus leucogenys)
Go to Gene View: RORC
Go to UniProtKB:  G1RH57
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
82O
Query on 82O

Download SDF File 
Download CCD File 
A, C, E, G
(3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl)cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide
C28 H39 N5 O2
NRAQMBSBKYAKMR-DVKRWUGUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.300α = 90.00
b = 72.600β = 89.98
c = 99.320γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references