9RHG | pdb_00009rhg

FZD7 in complex with negative allosteric modulator C407


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

In silico docking yields small molecule negative allosteric modulators targeting the core of Frizzled 7.

Scharf, M.M.Kinsolving, J.Gratz, L.Voss, J.H.Carrasco-Busturia, D.Forsberg, B.Kolb, P.Schulte, G.

(2025) Nat Commun 16: 11138-11138

  • DOI: https://doi.org/10.1038/s41467-025-67147-z
  • Primary Citation of Related Structures:  
    9RHG

  • PubMed Abstract: 

    Targeting the Frizzled family (FZD 1-10 ) of WNT receptors pharmacologically has, despite substantial therapeutic potential, proven difficult. Given an almost complete lack of validated, effective small molecules targeting FZDs, no putative ligand binding site has so far been identified. In order to target FZD 7 , a potential target for the treatment of intestinal tumors, we combine an approach of adapted docking setups and large molecular library docking screens, identifying compound C407. Applying pharmacological assays, genetically-encoded biosensors, site-directed mutagenesis, cryo-electron microscopy and molecular dynamics simulations, the compound binding site in the core of the seven transmembrane bundle is validated and C407 is confirmed as a negative allosteric modulator of WNT-induced and FZD-mediated WNT/β-catenin signaling. In summary, we provide here the proof-of-principle that targeting FZDs with small molecule compounds is possible and effective. Future hit optimization and functional validation in disease-relevant in vitro and in vivo models will pave the way towards clinical exploration.


  • Organizational Affiliation
    • Department of Physiology & Pharmacology, Sec Receptor Biology & Signaling, Biomedicum, Karolinska Institute, Stockholm, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Frizzled-7A [auth B],
B [auth A]
603Homo sapiensMutation(s): 0 
Gene Names: FZD7
UniProt & NIH Common Fund Data Resources
Find proteins for O75084 (Homo sapiens)
Explore O75084 
Go to UniProtKB:  O75084
PHAROS:  O75084
GTEx:  ENSG00000155760 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75084
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARCv4.7.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-04676
Swedish Research CouncilSweden2019-01190
Swedish Research CouncilSweden2024-02515
CancerfondenSwedenCAN2017/561
CancerfondenSweden20 1102 PjF
CancerfondenSweden23 2825 Pj
Novo Nordisk FoundationDenmarkNNF21OC0070008
Novo Nordisk FoundationDenmarkNNF22OC0078104
German Research Foundation (DFG)Germany504098926
German Research Foundation (DFG)Germany470002134
German Research Foundation (DFG)Germany520506488
Knut and Alice Wallenberg FoundationSwedenKAW 2020.0239
European Union (EU)European Union101199012
Swedish Research CouncilSweden2022-06725

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release