[English] 日本語
Yorodumi
- PDB-9pee: Cryo-EM structure of CCR6 bound by PF-07054894 and OXM2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9pee
TitleCryo-EM structure of CCR6 bound by PF-07054894 and OXM2
Components
  • (anti-BRIL Fab ...) x 2
  • Human CCR6
  • anti-BRIL Heavy chain
KeywordsMEMBRANE PROTEIN / GPCR / Complex / Antagonist
Function / homology: / :
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsWasilko, D.J. / Wu, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Med Chem / Year: 2025
Title: Discovery of PF-07054894, a Potent Squaramide-Based CCR6 Antagonist Displaying High CXCR2 Selectivity.
Authors: Mark E Schnute / Huixian Wu / John I Trujillo / Wei Li / David Jonathan Wasilko / Jennifer Alley / Eric P Arnold / Scott W Bagley / Gabriel Berstein / David C Blakemore / Mark W Bundesmann / ...Authors: Mark E Schnute / Huixian Wu / John I Trujillo / Wei Li / David Jonathan Wasilko / Jennifer Alley / Eric P Arnold / Scott W Bagley / Gabriel Berstein / David C Blakemore / Mark W Bundesmann / Gary M Chinigo / Chulho Choi / Robert Cooke / Kimberly Crouse / Alpay Dermenci / Theresa Dickinson / Andrew Flick / Richard K Frisbie / Carmen Garcia-Irizarry / Brian S Gerstenberger / David Hepworth / Neelu Kaila / Daniel W Kung / Daniel Lamb / Sophie Y Lavergne / David C Limburg / Shenping Liu / Vincent M Lombardo / Prolay K Mondal / James J Mousseau / Arjun Narayanan / Nootaree Niljianskul / Philippe Nuhant / Senliang Pan / Michael J Primiano / Mathieu Rappas / Daniel C Schmitt / Stefanus J Steyn / Ray Unwalla / Dipy Vasa / Michael L Vazquez / Fabien Vincent / Xiaojing Yang / Atli Thorarensen /
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 ...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 () which has advanced to clinical trials as a first in class approach targeting the receptor.
History
DepositionJul 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Human CCR6
L: anti-BRIL Fab Light chain
K: anti-BRIL Fab Nanobody
H: anti-BRIL Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4296
Polymers124,5544
Non-polymers8752
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Human CCR6


Mass: 54623.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

-
Antibody , 3 types, 3 molecules LKH

#2: Antibody anti-BRIL Fab Light chain


Mass: 25343.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody anti-BRIL Fab Nanobody


Mass: 15755.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Antibody anti-BRIL Heavy chain


Mass: 28832.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-A1A1W / N-{[(2R)-4-(bicyclo[1.1.1]pentan-1-yl)-5-oxomorpholin-2-yl]methyl}-1-[4-(trifluoromethyl)phenyl]cyclopropane-1-carboxamide


Mass: 408.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23F3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-A1CH1 / 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


Mass: 466.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30N6O4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex of Human CCR6/PF-07054894/OXM2 with anti-BRIL Fab and anti-BRIL Fab Nanobody
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Details: 50 mM HEPES pH 7.5, 150 mM NaCl, 0.003% LMNG, 0.0003% CHS, 50 uM OXM2 and 50 uM of PF-07054894
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: CCR6-BRIL/Fab/Nb complex co-purified with PF-07054894 and OXM2
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPUv2.12.1.2782RELimage acquisition
12cryoSPARC4.4.13D reconstruction
13PHENIX1.20_4459model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250839 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 9D3E

9d3e


Accession code: 9D3E / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.35 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047296
ELECTRON MICROSCOPYf_angle_d0.9729920
ELECTRON MICROSCOPYf_dihedral_angle_d5.4781041
ELECTRON MICROSCOPYf_chiral_restr0.0521120
ELECTRON MICROSCOPYf_plane_restr0.0081275

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more