6TJM | pdb_00006tjm

Crystal structure of an Estrogen Receptor alpha 8-mer phosphopeptide in complex with 14-3-3sigma stabilized by Pyrrolidone1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.218 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6TJM

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Design of Drug-Like Protein-Protein Interaction Stabilizers Guided By Chelation-Controlled Bioactive Conformation Stabilization.

Bosica, F.Andrei, S.A.Neves, J.F.Brandt, P.Gunnarsson, A.Landrieu, I.Ottmann, C.O'Mahony, G.

(2020) Chemistry 26: 7131-7139

  • DOI: https://doi.org/10.1002/chem.202001608
  • Primary Citation Related Structures: 
    6TJM, 6TL3

  • PubMed Abstract: 

    Protein-protein interactions (PPIs) of 14-3-3 proteins are a model system for studying PPI stabilization. The complex natural product Fusicoccin A stabilizes many 14-3-3 PPIs but is not amenable for use in SAR studies, motivating the search for more drug-like chemical matter. However, drug-like 14-3-3 PPI stabilizers enabling such studies have remained elusive. An X-ray crystal structure of a PPI in complex with an extremely low potency stabilizer uncovered an unexpected non-protein interacting, ligand-chelated Mg 2+ leading to the discovery of metal-ion-dependent 14-3-3 PPI stabilization potency. This originates from a novel chelation-controlled bioactive conformation stabilization effect. Metal chelation has been associated with pan-assay interference compounds (PAINS) and frequent hitter behavior, but chelation can evidently also lead to true potency gains and find use as a medicinal chemistry strategy to guide compound optimization. To demonstrate this, we exploited the effect to design the first potent, selective, and drug-like 14-3-3 PPI stabilizers.


  • Organizational Affiliation
    • Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden.

Macromolecule Content 

  • Total Structure Weight: 27.92 kDa 
  • Atom Count: 2,056 
  • Modeled Residue Count: 234 
  • Deposited Residue Count: 245 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein sigma236Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
GTEx:  ENSG00000175793 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31947
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
C-terminal phosphopeptide of human estrogen receptor alpha9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups
UniProt GroupP03372
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NE5
(Subject of Investigation/LOI)

Query on NE5



Download:Ideal Coordinates CCD File
D [auth A]5-[(2R)-3-benzoyl-4-hydroxy-2-(4-nitrophenyl)-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]-2-hydroxybenzoic acid
C24 H16 N2 O8
SHWIONPIUOUFNT-HXUWFJFHSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.218 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.841α = 90
b = 152.31β = 90
c = 76.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionNetherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary
  • Version 2.0: 2026-04-15
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary