7PWZ | pdb_00007pwz

Crystal structure of 14-3-3 sigma in complex with a C-terminal Estrogen Receptoralpha phosphopeptide, stabilised by Pyrrolidone1 derivative 228

• PDB DOI: https://doi.org/10.2210/pdb7PWZ/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-07 Released: 2022-12-21 
• Deposition Author(s): Andrei, S.A., Bosica, F., O'Mahony, G., Ottmann, C.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission, Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.298 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Designing Selective Drug-like Molecular Glues for the Glucocorticoid Receptor/14-3-3 Protein-Protein Interaction.

Pallesen, J.S., Munier, C.C., Bosica, F., Andrei, S.A., Edman, K., Gunnarsson, A., La Sala, G., Putra, O.D., Srdanovic, S., Wilson, A.J., Wissler, L., Ottmann, C., Perry, M.W.D., O'Mahony, G.

(2022) J Med Chem 65: 16818-16828

• PubMed: 36484727 
• DOI: https://doi.org/10.1021/acs.jmedchem.2c01635
• Primary Citation Related Structures: 
  7PWT, 7PWZ, 8A9G


• PubMed Abstract: 
  

  The ubiquitously expressed glucocorticoid receptor (GR) is a nuclear receptor that controls a broad range of biological processes and is activated by steroidal glucocorticoids such as hydrocortisone or dexamethasone. Glucocorticoids are used to treat a wide variety of conditions, from inflammation to cancer but suffer from a range of side effects that motivate the search for safer GR modulators. GR is also regulated outside the steroid-binding site through protein-protein interactions (PPIs) with 14-3-3 adapter proteins. Manipulation of these PPIs will provide insights into noncanonical GR signaling as well as a new level of control over GR activity. We report the first molecular glues that selectively stabilize the 14-3-3/GR PPI using the related nuclear receptor estrogen receptor α (ERα) as a selectivity target to drive design. These 14-3-3/GR PPI stabilizers can be used to dissect noncanonical GR signaling and enable the development of novel atypical GR modulators.

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Organizational Affiliation: 
• Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden.
Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden.
Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.
Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden.
Early Product Development and Manufacturing, Pharmaceutical Sciences R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden.
School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, West Yorkshire LS2 9JT, U.K.

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: 27.91 kDa 
• Atom Count: 2,087 
• Modeled Residue Count: 231 
• Deposited Residue Count: 244 
• 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
C-terminus of Estrogen receptor alpha	B	8	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8CQ (Subject of Investigation/LOI)	D [auth A]	2-oxidanyl-5-[(2~{R})-4-oxidanyl-5-oxidanylidene-2-(1-oxidanylidene-3~{H}-2-benzofuran-5-yl)-3-(phenylcarbonyl)-2~{H}-pyrrol-1-yl]benzoic acid C26 H17 N O8 KRAIUTVUTRGUAY-OAQYLSRUSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 2.50 Å
• R-Value Free:  0.298 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.173	α = 90
b = 151.615	β = 90
c = 78.945	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-21 
Deposition Author(s): Andrei, S.A., Bosica, F., O'Mahony, G., Ottmann, C.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	Netherlands	675179
Netherlands Organisation for Scientific Research (NWO)	Netherlands	717.014.001

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2023-01-04
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary