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- PDB-9oo7: Human PORCN bound to inhibitor ETC159 -

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Basic information

Entry
Database: PDB / ID: 9oo7
TitleHuman PORCN bound to inhibitor ETC159
ComponentsIsoform 3 of Protein-serine O-palmitoleoyltransferase porcupine,Green fluorescent protein
KeywordsMEMBRANE PROTEIN / transmembrane protein / MBOAT / acylase / Wnt acylase / enzyme / ER
Function / homology
Function and homology information


[Wnt protein] O-palmitoleoyl transferase / protein palmitoleylation / palmitoleoyltransferase activity / LGK974 inhibits PORCN / protein lipidation / Wnt protein secretion / lipid modification / glycoprotein metabolic process / WNT ligand biogenesis and trafficking / Wnt-protein binding ...[Wnt protein] O-palmitoleoyl transferase / protein palmitoleylation / palmitoleoyltransferase activity / LGK974 inhibits PORCN / protein lipidation / Wnt protein secretion / lipid modification / glycoprotein metabolic process / WNT ligand biogenesis and trafficking / Wnt-protein binding / AMPA glutamate receptor complex / regulation of postsynaptic membrane neurotransmitter receptor levels / bioluminescence / generation of precursor metabolites and energy / Wnt signaling pathway / endoplasmic reticulum membrane / glutamatergic synapse / endoplasmic reticulum / membrane
Similarity search - Function
: / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
: / Green fluorescent protein / Protein-serine O-palmitoleoyltransferase porcupine
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsBlack, K.A. / Venugopal, H. / Glukhova, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other private Australia
CitationJournal: Commun Chem / Year: 2025
Title: Structural basis for Porcupine inhibition.
Authors: Katrina A Black / Jesse I Mobbs / Hariprasad Venugopal / Toby A Dite / Andrew Leis / Lilian Ll Wong / Laura F Dagley / David M Thal / Alisa Glukhova /
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)- ...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.
History
DepositionMay 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Protein-serine O-palmitoleoyltransferase porcupine,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2153
Polymers81,7581
Non-polymers4572
Water543
1


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

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Components

#1: Protein Isoform 3 of Protein-serine O-palmitoleoyltransferase porcupine,Green fluorescent protein / Protein MG61


Mass: 81758.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PORCN, MG61, PORC, PPN, GFP / Production host: Homo sapiens (human)
References: UniProt: Q9H237, UniProt: P42212, [Wnt protein] O-palmitoleoyl transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1CC6 / 2-(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)-N-(6-phenylpyridazin-3-yl)acetamide


Mass: 391.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17N7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human Porcupine with inhibitor C59 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.081 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92221 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 59.42 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00423589
ELECTRON MICROSCOPYf_angle_d0.75754886
ELECTRON MICROSCOPYf_chiral_restr0.0461545
ELECTRON MICROSCOPYf_plane_restr0.0138602
ELECTRON MICROSCOPYf_dihedral_angle_d12.41711241

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