9SA9 | pdb_00009sa9

14-3-3sigma protein binding to macrocycle 2

• PDB DOI: https://doi.org/10.2210/pdb9SA9/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-07 Released: 2026-01-14 
• Deposition Author(s): Pennings, M.A.M., van den Bosch, M.A.W., Brunsveld, L.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.201 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Macrocyclic Molecular Glues for the 14-3-3/ChREBP Interaction: Affinity and Cooperativity in an Inverse Relationship.

Pennings, M.A.M., van den Bosch, M.A.W., Oberheide, A., Verhoef, C.J.A., Ottmann, C., Markvoort, A.J., Miley, G.P., Brunsveld, L.

(2025) Angew Chem Int Ed Engl : e21678-e21678

• PubMed: 41414041 
• DOI: https://doi.org/10.1002/anie.202521678
• Primary Citation of Related Structures:  
  9SA9, 9SAB, 9SAE


• PubMed Abstract: 
  

  Molecular glues (MGs) stabilize protein-protein interactions (PPIs) by simultaneously binding two or more proteins at their composite interface. Macrocycles present attractive properties as MGs, including large contact surfaces to address the often flat and undefined composite PPI interfaces, but their structure-based design has remained intangible. We have designed peptidomimetic macrocycles capable of enhancing the PPI between 14-3-3 and the carbohydrate response element binding protein (ChREBP), a regulatory transcription factor. Biophysical characterization of these MGs revealed the importance of optimized linker length, displaying a reduced entropic cost compared to the linear counterparts, while preserving key contacts with 14-3-3. Binding assays demonstrated that the macrocycles selectively and cooperatively stabilized the 14-3-3/ChREBP complex, with an intriguing inverse relationship between intrinsic binding affinity to 14-3-3 and cooperativity in PPI stabilization. Ternary co-crystal structures of the macrocycles binding at the composite 14-3-3/ChREBP interface provided a molecular rationale for the affinity and cooperativity differences. Overall, this study highlights structural, kinetic, and thermodynamic features that guide effective macrocyclic MG design and brings forward the crucial interplay of affinity and cooperativity in stabilizing PPIs.

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Organizational Affiliation: 
• Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, 5600MB, The Netherlands.
Synthetic Biology Group, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, 5600MB, The Netherlands.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.96 kDa 
• Atom Count: 4,198 
• Modeled Residue Count: 474 
• Deposited Residue Count: 486 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	236	Homo sapiens	Mutation(s): 0  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	B [auth L]	236	Homo sapiens	Mutation(s): 0  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrocycle 2	C, D	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A], H [auth L], I [auth L], J [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A], K [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PPN	C, D	L-PEPTIDE LINKING	C9 H10 N2 O4		PHE
SEP	C, D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.201 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.308	α = 90
b = 70.401	β = 90
c = 128.166	γ = 90

Software Package:

Software Name	Purpose
PDB-REDO	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Pennings, M.A.M., van den Bosch, M.A.W., Brunsveld, L.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	OCenW.M20.200

Revision History  

• Version 1.0: 2026-01-14
  Type: Initial release