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TitleStructural basis for Porcupine inhibition.
Journal, issue, pagesCommun Chem, Vol. 8, Issue 1, Page 348, Year 2025
Publish dateNov 12, 2025
AuthorsKatrina A Black / Jesse I Mobbs / Hariprasad Venugopal / Toby A Dite / Andrew Leis / Lilian Ll Wong / Laura F Dagley / David M Thal / Alisa Glukhova /
PubMed AbstractWnt 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)- ...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.
External linksCommun Chem / PubMed:41225132 / PubMed Central
MethodsEM (single particle)
Resolution2.39 - 3.32 Å
Structure data

70660

9oo6

EMDB-70660, PDB-9oo6:
Human PORCN bound to inhibitor C59
Method: EM (single particle) / Resolution: 2.39 Å

70661

9oo7

EMDB-70661, PDB-9oo7:
Human PORCN bound to inhibitor ETC159
Method: EM (single particle) / Resolution: 2.61 Å

70662

9oo8

EMDB-70662, PDB-9oo8:
Apo Human PORCN
Method: EM (single particle) / Resolution: 3.32 Å

Chemicals

PDB-1cc5:
CRYSTAL STRUCTURE OF AZOTOBACTER CYTOCHROME C5 AT 2.5 ANGSTROMS RESOLUTION

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

PDB-1cc6:
PHE161 AND ARG166 VARIANTS OF P-HYDROXYBENZOATE HYDROXYLASE. IMPLICATIONS FOR NADPH RECOGNITION AND STRUCTURAL STABILITY.

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / transmembrane protein / MBOAT / acylase / Wnt acylase / enzyme / ER

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