Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.22 kDa 
• Atom Count: 3807 
• Modelled Residue Count: 455 
• Deposited Residue Count: 456 
• Unique protein chains: 1

6B31

Structure of RORgt in complex with a novel inverse agonist 2

• PDB DOI: 10.2210/pdb6B31/pdb

• Classification: signaling protein/agonist
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-20 Released: 2018-08-01 
• Deposition Author(s): Skene, R.J., Hoffman, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 0.245 
• R-Value Work: 0.161 
• R-Value Observed: 0.165 

Literature

Identification of novel quinazolinedione derivatives as ROR gamma t inverse agonist.

Fukase, Y., Sato, A., Tomata, Y., Ochida, A., Kono, M., Yonemori, K., Koga, K., Okui, T., Yamasaki, M., Fujitani, Y., Nakagawa, H., Koyama, R., Nakayama, M., Skene, R., Sang, B.C., Hoffman, I., Shirai, J., Yamamoto, S.

(2018) Bioorg Med Chem 26: 721-736

• PubMed: 29342416 
• DOI: 10.1016/j.bmc.2017.12.039
• Primary Citation of Related Structures:  
  6B31


• PubMed Abstract: 
  

Novel small molecules were synthesized and evaluated as retinoic acid receptor-related orphan receptor-gamma t (RORγt) inverse agonists for the treatment of inflammatory and autoimmune diseases. A hit compound, 1, was discovered by high-throughput screening of our compound library. The structure-activity relationship (SAR) study of compound 1 showed that the introduction of a chlorine group at the 3-position of 4-cyanophenyl moiety increased the potency and a 3-methylpentane-1,5-diamide linker is favorable for the activity. The carbazole moiety of 1 was also optimized; a quinazolinedione derivative 18i suppressed the increase of IL-17A mRNA level in the lymph node of a rat model of experimental autoimmune encephalomyelitis (EAE) upon oral administration. These results indicate that the novel quinazolinedione derivatives have great potential as orally available small-molecule RORγt inverse agonists for the treatment of Th17-driven autoimmune diseases. A U-shaped bioactive conformation of this chemotype with RORγt protein was also observed.

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Organizational Affiliation: 

Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B	228	Homo sapiens	Mutation(s): 0  Gene Names: RORC, NR1F3, RORG, RZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens) Explore P51449  Go to UniProtKB:  P51449
PHAROS:  P51449

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CFJ (Subject of Investigation/LOI)	C [auth A], D [auth B]	(3S)-N~1~-(3-chloro-4-cyanophenyl)-N~5~-(1,3-diethyl-2,4-dioxo-1,2,3,4-tetrahydroquinazolin-6-yl)-3-methylpentanediamide C25 H26 Cl N5 O4 BOZDOTVXHRNQKE-HNNXBMFYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CFJ	BindingDB:  6B31	IC50: min: 3.6, max: 47 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 0.245 
• R-Value Work: 0.161 
• R-Value Observed: 0.165 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.428	α = 90
b = 96.428	β = 90
c = 130.846	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-09-20 
• Released Date: 2018-08-01 
Deposition Author(s): Skene, R.J., Hoffman, I.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release