4WQP | pdb_00004wqp

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

• PDB DOI: https://doi.org/10.2210/pdb4WQP/pdb

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


• Deposited: 2014-10-22 Released: 2015-01-14 
• Deposition Author(s): Boenig, G., Hymowitz, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.180 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Minor Structural Change to Tertiary Sulfonamide RORc Ligands Led to Opposite Mechanisms of Action.

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

(2015) ACS Med Chem Lett 6: 276-281

• PubMed: 25815138 
• DOI: https://doi.org/10.1021/ml500420y
• Primary Citation Related Structures: 
  4WPF, 4WQP


• PubMed Abstract: 
  

  A minor structural change to tertiary sulfonamide RORc ligands led to distinct mechanisms of action. Co-crystal structures of two compounds revealed mechanistically consistent protein conformational changes. Optimized phenylsulfonamides were identified as RORc agonists while benzylsulfonamides exhibited potent inverse agonist activity. Compounds behaving as agonists in our biochemical assay also gave rise to an increased production of IL-17 in human PBMCs whereas inverse agonists led to significant suppression of IL-17 under the same assay conditions. The most potent inverse agonist compound showed >180-fold selectivity over the ROR isoforms as well as all other nuclear receptors that were profiled.

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Organizational Affiliation: 
• Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.
Argenta, Early Discovery, Charles River, 7-9 Spire Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, U.K.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.42 kDa 
• Atom Count: 4,205 
• Modeled Residue Count: 468 
• Deposited Residue Count: 543 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B	265	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VAL-GLU-ARG-LEU-GLN-ILE-PHE-GLN-HIS-LEU-HIS-PRO-ILE	C [auth P]	13	Homo sapiens	Mutation(s): 0  Gene Names: Nuclear receptor ROR-gamma
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
3SX	D [auth A], F [auth B]	N-[4-(4-acetylpiperazin-1-yl)benzyl]-N-(2-methylpropyl)-1-phenylmethanesulfonamide C24 H33 N3 O3 S CYRKYCCPWKLCDV-UHFFFAOYSA-N
SO4	E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
3SX	BindingDB:  4WQP	IC50: 47 (nM) from 1 assay(s)
		EC50: min: 57, max: 120 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.180 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.735	α = 90
b = 99.735	β = 90
c = 129.606	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Boenig, G., Hymowitz, S.G.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references
• Version 1.2: 2015-04-22
  Changes: Database references
• Version 2.0: 2023-12-27
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Source and taxonomy