4QM0

Crystal structure of RORc in complex with a tertiary sulfonamide inverse agonist

• PDB DOI: https://doi.org/10.2210/pdb4QM0/pdb

• Classification: Transcription/Transcription inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-14 Released: 2014-09-17 
• Deposition Author(s): Boenig, G., Hymowitz, S.G., Wang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.186 

Literature

Reduction in lipophilicity improved the solubility, plasma-protein binding, and permeability of tertiary sulfonamide RORc inverse agonists.

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

(2014) Bioorg Med Chem Lett 24: 3891-3897

• PubMed: 25017032 
• DOI: https://doi.org/10.1016/j.bmcl.2014.06.048
• Primary Citation of Related Structures:  
  4QM0


• PubMed Abstract: 
  

  Using structure-based drug design principles, we identified opportunities to reduce the lipophilicity of our tertiary sulfonamide RORc inverse agonists. The new analogs possessed improved RORc cellular potencies with >77-fold selectivity for RORc over other nuclear receptors in our cell assay suite. The reduction in lipophilicity also led to an increased plasma-protein unbound fraction and improvements in cellular permeability and aqueous solubility.

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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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.19 kDa 
• Atom Count: 4,147 
• Modelled Residue Count: 470 
• 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 [auth C]	251	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
39K	C [auth A], E [auth C]	N-(2-methylpropyl)-N-({5-[4-(methylsulfonyl)phenyl]thiophen-2-yl}methyl)-1-phenylmethanesulfonamide C23 H27 N O4 S3 RXMHSSANSKRGOG-UHFFFAOYSA-N
DMS	D [auth A], F [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
39K	BindingDB:  4QM0	IC50: 130 (nM) from 1 assay(s)
		EC50: min: 460, max: 1000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.186 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.051	α = 90
b = 99.051	β = 90
c = 129.666	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Boenig, G., Hymowitz, S.G., Wang, W.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations