8FAV

HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 5 ANDINDAZOLE ACID BOUND IN H12-POCKET

• PDB DOI: https://doi.org/10.2210/pdb8FAV/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-11-28 Released: 2023-03-01 
• Deposition Author(s): Vajdos, F.F.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.233 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Macrocyclic Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonists.

Schnute, M.E., Trujillo, J.I., Lee, K.L., Unwalla, R., Vajdos, F.F., Kauppi, B., Nuhant, P., Flick, A.C., Crouse, K.K., Zhao, Y., Samuel, A., Lombardo, V., Taylor, A.P., Brault, A.L., Knafels, J.D., Vazquez, M.L., Berstein, G.

(2023) ACS Med Chem Lett 14: 191-198

• PubMed: 36793423 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00500
• Primary Citation of Related Structures:  
  8FAV, 8FB1, 8FB2


• PubMed Abstract: 
  

  Macrocyclic retinoic acid receptor-related orphan receptor C2 (RORC2) inverse agonists have been designed with favorable properties for topical administration. Inspired by the unanticipated bound conformation of an acyclic sulfonamide-based RORC2 ligand from cocrystal structure analysis, macrocyclic linker connections between the halves of the molecule were explored. Further optimization of analogues was accomplished to maximize potency and refine physiochemical properties (MW, lipophilicity) best suited for topical application. Compound 14 demonstrated potent inhibition of interleukin-17A (IL-17A) production by human Th17 cells and in vitro permeation through healthy human skin achieving high total compound concentration in both skin epidermis and dermis layers.

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Organizational Affiliation: 

Medicine Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States.

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: 62.48 kDa 
• Atom Count: 4,523 
• Modelled Residue Count: 496 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B	262	Homo sapiens	Mutation(s): 2  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4Y5	D [auth A], G [auth B]	4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-4-fluoro-1H-indazol-3-yl}-3-fluorobenzoic acid C22 H10 Cl F5 N2 O3 PFVOSXMQCIFOSO-UHFFFAOYSA-N
LKY (Subject of Investigation/LOI)	C [auth A], F [auth B]	3-cyano-N-(3-{[(3S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl]methyl}-5-fluoro-2-methylphenyl)benzamide C27 H31 F N4 O2 AQGBWBMWWNRWNU-SFHVURJKSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.233 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.088	α = 90
b = 96.922	β = 91.26
c = 56.914	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-01 
Deposition Author(s): Vajdos, F.F.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2023-03-01
  Type: Initial release