9OO6 | pdb_00009oo6

Human PORCN bound to inhibitor C59


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis for Porcupine inhibition.

Black, K.A.Mobbs, J.I.Venugopal, H.Dite, T.A.Leis, A.Wong, L.L.Dagley, L.F.Thal, D.M.Glukhova, A.

(2025) Commun Chem 8: 348-348

  • DOI: https://doi.org/10.1038/s42004-025-01726-5
  • Primary Citation of Related Structures:  
    9OO6, 9OO7, 9OO8

  • PubMed Abstract: 

    Wnt signalling is essential for embryonic development and tissue homeostasis, and its dysregulation is associated with multiple types of cancer. Porcupine (PORCN), an endoplasmic reticulum (ER)-resident membrane-bound O-acyltransferase, catalyses the palmitoleoylation of all 19 human Wnts-a critical modification required for their secretion and activity. This central role makes PORCN an attractive therapeutic target for Wnt-driven cancers, with several inhibitors currently in clinical trials. Here, we present high-resolution cryo-electron microscopy structures of human PORCN in complex with the inhibitors C59 (2.4 Å) and ETC159 (2.6 Å), as well as in a ligand-free state (3.3 Å). These structures reveal critical ordered water molecules that form a hydrogen-bonding network within the active site, mediating inhibitor binding. Our docking simulations of diverse PORCN inhibitors demonstrate that despite their different chemical scaffolds, these compounds adopt similar conformations within the acyl-CoA binding site and are also engaged through a conserved water molecule. Our findings provide a structural foundation for the rational design of next-generation PORCN inhibitors with improved pharmacological properties for cancer therapy.


  • Organizational Affiliation
    • The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of Protein-serine O-palmitoleoyltransferase porcupine,Green fluorescent protein725Homo sapiensMutation(s): 0 
Gene Names: PORCNMG61PORCPPNGFP
EC: 2.3.1.250
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H237 (Homo sapiens)
Go to UniProtKB:  Q9H237
PHAROS:  Q9H237
GTEx:  ENSG00000102312 
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212Q9H237-3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateAustralia--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release