9PEE | pdb_00009pee

Cryo-EM structure of CCR6 bound by PF-07054894 and OXM2

• PDB DOI: https://doi.org/10.2210/pdb9PEE/pdb
• EM Map EMD-71559: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-07-02 Released: 2025-10-01 
• Deposition Author(s): Wasilko, D.J., Wu, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Discovery of PF-07054894, a Potent Squaramide-Based CCR6 Antagonist Displaying High CXCR2 Selectivity.

Schnute, M.E., Wu, H., Trujillo, J.I., Li, W., Wasilko, D.J., Alley, J., Arnold, E.P., Bagley, S.W., Berstein, G., Blakemore, D.C., Bundesmann, M.W., Chinigo, G.M., Choi, C., Cooke, R., Crouse, K., Dermenci, A., Dickinson, T., Flick, A., Frisbie, R.K., Garcia-Irizarry, C., Gerstenberger, B.S., Hepworth, D., Kaila, N., Kung, D.W., Lamb, D., Lavergne, S.Y., Limburg, D.C., Liu, S., Lombardo, V.M., Mondal, P.K., Mousseau, J.J., Narayanan, A., Niljianskul, N., Nuhant, P., Pan, S., Primiano, M.J., Rappas, M., Schmitt, D.C., Steyn, S.J., Unwalla, R., Vasa, D., Vazquez, M.L., Vincent, F., Yang, X., Thorarensen, A.

(2025) J Med Chem 68: 20689-20716

• PubMed: 40977184 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c01946
• Primary Citation of Related Structures:  
  9PEE


• PubMed Abstract: 
  

  The G protein-coupled receptor (GPCR) CCR6 mediates the migration of pathogenic immune cells to the site of inflammation in response to the chemokine CCL20. CCR6 is an attractive target for the treatment of chronic autoimmune disease as antagonism of the receptor is expected to block CCL20-mediated immune cell recruitment. High-throughput-screening identified a squaramide-based, allosteric antagonist of CCR6 that potently inhibited CCL20-mediated T cell chemotaxis, but it also inhibited CXCL1-mediated neutrophil chemotaxis through CXCR2 antagonism. Lead optimization achieved differentiation from CXCR2 through identification of a methyl substituent-dependent selectivity switch or "magic methyl for selectivity". The mechanism for this effect is rooted in different antagonist-induced ligand-receptor behaviors, insurmountable for CCR6 and surmountable for CXCR2. Herein, we report the discovery and preclinical evaluation of the CCR6 antagonist PF-07054894 ( 18l ) which has advanced to clinical trials as a first in class approach targeting the receptor.

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Organizational Affiliation: 
• Medicine Design, Pfizer Inc, Cambridge, Massachusetts 02139, United States.
Medicine Design, Pfizer Inc, Groton, Connecticut 06340, United States.
Inflammation and Immunology Research, Pfizer Inc, Cambridge, Massachusetts 02139, United States.
Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom.
Drug Product Design, Pfizer Inc, Cambridge, Massachusetts 02139, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 125.43 kDa 
• Atom Count: 7,133 
• Modeled Residue Count: 915 
• Deposited Residue Count: 1,123 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human CCR6	A	480	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Fab Light chain	B [auth L]	233	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Fab Nanobody	C [auth K]	141	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-BRIL Heavy chain	D [auth H]	269	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CH1 (Subject of Investigation/LOI)	F [auth A]	4-[(2-{[(R)-(1,4-dimethyl-1H-pyrazol-3-yl)(1-methylcyclopentyl)methyl]amino}-3,4-dioxocyclobut-1-en-1-yl)amino]-3-hydroxy-N,N-dimethylpyridine-2-carboxamide C24 H30 N6 O4 WZBSYWCLIMRAHO-QFIPXVFZSA-N
A1A1W (Subject of Investigation/LOI)	E [auth A]	N-{[(2R)-4-(bicyclo[1.1.1]pentan-1-yl)-5-oxomorpholin-2-yl]methyl}-1-[4-(trifluoromethyl)phenyl]cyclopropane-1-carboxamide C21 H23 F3 N2 O3 MGXLQVNOTOHKMK-VVFCZOMOSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.1
MODEL REFINEMENT	PHENIX	1.20_4459

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Wasilko, D.J., Wu, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release
  
• Version 1.1: 2025-10-08
  Changes: Data collection, Database references
• Version 1.2: 2025-10-22
  Changes: Data collection, Database references