5ETH | pdb_00005eth

RORy in complex with inverse agonist 3.

• PDB DOI: https://doi.org/10.2210/pdb5ETH/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-17 Released: 2016-04-27 
• Deposition Author(s): Marcotte, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.284 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Discovery of biaryls as ROR gamma inverse agonists by using structure-based design.

Enyedy, I.J., Powell, N.A., Caravella, J., van Vloten, K., Chao, J., Banerjee, D., Marcotte, D., Silvian, L., McKenzie, A., Hong, V.S., Fontenot, J.D.

(2016) Bioorg Med Chem Lett 26: 2459-2463

• PubMed: 27080181 
• DOI: https://doi.org/10.1016/j.bmcl.2016.03.109
• Primary Citation Related Structures: 
  5EJV, 5ETH


• PubMed Abstract: 
  

  RORγ plays a critical role in controlling a pro-inflammatory gene expression program in several lymphocyte lineages including T cells, γδ T cells, and innate lymphoid cells. RORγ-mediated inflammation has been linked to susceptibility to Crohn's disease, arthritis, and psoriasis. Thus inverse agonists of RORγ have the potential of modulating inflammation. Our goal was to optimize two RORγ inverse agonists: T0901317 from literature and 1 that we obtained from internal screening. We used information from internal X-ray structures to design two libraries that led to a new biaryl series.

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Organizational Affiliation: 
• Biogen, 250 Binney St., Cambridge, MA 02142, USA. Electronic address: [e-mail].
Biogen, 250 Binney St., Cambridge, MA 02142, USA.
Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.09 kDa 
• Atom Count: 3,569 
• Modeled Residue Count: 439 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B	223	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 GTEx:  ENSG00000143365

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5RT	C [auth A], D [auth B]	1-methyl-~{N}-(1-thiophen-2-ylcarbonyl-3,4-dihydro-2~{H}-quinolin-6-yl)-~{N}-[2,2,2-tris(fluoranyl)ethyl]indole-4-sulfonamide C25 H22 F3 N3 O3 S2 MGKISJPOEOHZCS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5RT	BindingDB:  5ETH	IC50: 56 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.284 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.559	α = 90
b = 56.413	β = 124.67
c = 77.922	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
Coot	model building
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Marcotte, D.M.

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description