8A9G | pdb_00008a9g

Binary complex of 14-3-3 zeta Glucocorticoid Receptor (GR) pT524 peptide stabilised by (R)-para chloropyrrolidone1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.261 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QJKClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01635
  • Primary Citation of 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.


  • Organizational Affiliation

    Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein zeta/delta
A, B
235Homo sapiensMutation(s): 0 
Gene Names: YWHAZ
UniProt & NIH Common Fund Data Resources
Find proteins for P63104 (Homo sapiens)
Explore P63104 
Go to UniProtKB:  P63104
PHAROS:  P63104
GTEx:  ENSG00000164924 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63104
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glucocorticoid receptor
C, D
13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
PHAROS:  P04150
GTEx:  ENSG00000113580 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04150
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QJK (Subject of Investigation/LOI)
Query on QJK

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
5-[(2~{R})-3-(4-chlorophenyl)carbonyl-2-(4-nitrophenyl)-4-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-1-yl]-2-oxidanyl-benzoic acid
C24 H15 Cl N2 O8
JNIFVXVQHFKKPJ-HXUWFJFHSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
C, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.261 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.35α = 90
b = 78.07β = 90
c = 122.57γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QJKClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean Union675179

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    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: 2024-11-13
    Changes: Structure summary