4NB6 | pdb_00004nb6

Crystal structure of the ligand binding domain of RORC with T0901317

• PDB DOI: https://doi.org/10.2210/pdb4NB6/pdb

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


• Deposited: 2013-10-22 Released: 2013-11-27 
• Deposition Author(s): Hymowitz, S.G., Boenig-de Leon, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.270 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of substituted hexafluoroisopropanol-arylsulfonamides as modulators of RORc.

Fauber, B.P., de Leon Boenig, G., Burton, B., Eidenschenk, C., Everett, C., Gobbi, A., Hymowitz, S.G., Johnson, A.R., Liimatta, M., Lockey, P., Norman, M., Ouyang, W., Rene, O., Wong, H.

(2013) Bioorg Med Chem Lett 23: 6604-6609

• PubMed: 24239186 
• DOI: https://doi.org/10.1016/j.bmcl.2013.10.054
• Primary Citation Related Structures: 
  4NB6


• PubMed Abstract: 
  

  The structure-activity relationships of T0901317 analogs were explored as RORc inverse agonists using the principles of property- and structure-based drug design. An X-ray co-crystal structure of T0901317 and RORc was obtained and provided molecular insight into why T0901317 functioned as an inverse agonist of RORc; whereas, the same ligand functioned as an agonist of FXR, LXR, and PXR. The structural data was also used to design inhibitors with improved RORc biochemical and cellular activities. The improved inhibitors possessed enhanced selectivity profiles (rationalized using the X-ray crystallographic data) against other nuclear receptors.

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Organizational Affiliation: 
• Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 59.05 kDa 
• Atom Count: 3,711 
• Modeled Residue Count: 443 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B	251	Homo sapiens	Mutation(s): 0  Gene Names: NR1F3, RORC, 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
444	C [auth A], D [auth B]	N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE C17 H12 F9 N O3 S SGIWFELWJPNFDH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
444	BindingDB:  4NB6	Ki: 51 (nM) from 1 assay(s)
		IC50: min: 60, max: 6500 (nM) from 15 assay(s)
		EC50: min: 54, max: 463 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.270 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.534	α = 90
b = 99.534	β = 90
c = 125.777	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Hymowitz, S.G., Boenig-de Leon, G.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description