9I70 | pdb_00009i70

14-3-3sigma binding to the ERa peptide and compound 17

• PDB DOI: https://doi.org/10.2210/pdb9I70/pdb

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


• Deposited: 2025-01-31 Released: 2025-07-30 
• Deposition Author(s): Pennings, M.A.M., Arkin, M.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.147 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.120 (Depositor) 
• R-Value Observed: 
  0.121 (Depositor) 

Starting Model: experimental

Literature

Scaffold-hopping for molecular glues targeting the 14-3-3/ER alpha complex.

Konstantinidou, M., Zingiridis, M., Pennings, M.A.M., Fragkiadakis, M., Virta, J.M., Revalde, J.L., Visser, E.J., Ottmann, C., Brunsveld, L., Neochoritis, C.G., Arkin, M.R.

(2025) Nat Commun 16: 6467-6467

• PubMed: 40659654 
• DOI: https://doi.org/10.1038/s41467-025-61176-4
• Primary Citation Related Structures: 
  9I6S, 9I6T, 9I6U, 9I6V, 9I6W, 9I6X, 9I6Y, 9I6Z, 9I70, 9I71, 9I72, 9I73, 9I74, 9I75


• PubMed Abstract: 
  

  Molecular glues, small molecules that bind cooperatively at a protein-protein interface, have emerged as powerful modalities for the modulation of protein-protein interactions (PPIs) and "undruggable" targets. The systematic identification of new chemical matter with a molecular glue mechanism of action remains a significant challenge in drug discovery. Here, we present a scaffold hopping approach, using as a starting point our previously developed molecular glues for the native 14-3-3/estrogen receptor alpha (ERα) complex. The novel, computationally designed scaffold is based on the Groebke-Blackburn-Bienaymé multi-component reaction (MCR), leading to drug-like analogs with multiple points of variation, thus enabling the rapid derivatization and optimization of the scaffold. Structure-activity relationships (SAR) are developed using orthogonal biophysical assays, such as intact mass spectrometry, TR-FRET and SPR. Rational structure-guided optimization is facilitated by multiple crystal structures of ternary complexes with the glues, 14-3-3 and phospho-peptides mimicking the highly disordered C-terminus of ERα. Cellular stabilization of 14-3-3/ERα for the most potent analogs is confirmed using a NanoBRET assay with full-length proteins in live cells. Our approach highlights the potential of MCR chemistry, combined with scaffold hopping, to drive the development and optimization of unprecedented molecular glue scaffolds.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC) University of California San Francisco (UCSF), San Francisco, CA, USA. [e-mail].
Department of Chemistry University of Crete Voutes, Heraklion, Greece.
Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands.
Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC) University of California San Francisco (UCSF), San Francisco, CA, USA.
Department of Chemistry University of Crete Voutes, Heraklion, Greece. [e-mail].
Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC) University of California San Francisco (UCSF), San Francisco, CA, USA. [e-mail].

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.76 kDa 
• Atom Count: 2,291 
• Modeled Residue Count: 241 
• Deposited Residue Count: 241 
• Unique protein chains: 2

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
Estrogen receptor	B	5	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1I0X (Subject of Investigation/LOI)	E [auth A]	2-chloranyl-~{N}-[4-[3-[(2,6-dimethylphenyl)amino]imidazo[1,2-a]pyridin-2-yl]phenyl]ethanamide C23 H21 Cl N4 O FYRGYUTXZAJRES-UHFFFAOYSA-N
CA	C [auth A], D [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.147 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.120 (Depositor) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.271	α = 90
b = 112.487	β = 90
c = 62.646	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Pennings, M.A.M., Arkin, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM147696

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release