6BJN

PICK1 PDZ domain in complex with the class I PDZ binding motif QSAV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lock and chop: A novel method for the generation of a PICK1 PDZ domain and piperidine-based inhibitor co-crystal structure.

Marcotte, D.J.Hus, J.C.Banos, C.C.Wildes, C.Arduini, R.Bergeron, C.Hession, C.A.Baker, D.P.Lin, E.Guckian, K.M.Dunah, A.W.Silvian, L.F.

(2018) Protein Sci. 27: 672-680

  • DOI: 10.1002/pro.3361
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The membrane protein interacting with kinase C1 (PICK1) plays a trafficking role in the internalization of neuron receptors such as the amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) receptor. Reduction of surface AMPA type receptors on neur ...

    The membrane protein interacting with kinase C1 (PICK1) plays a trafficking role in the internalization of neuron receptors such as the amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) receptor. Reduction of surface AMPA type receptors on neurons reduces synaptic communication leading to cognitive impairment in progressive neurodegenerative diseases such as Alzheimer disease. The internalization of AMPA receptors is mediated by the PDZ domain of PICK1 which binds to the GluA2 subunit of AMPA receptors and targets the receptor for internalization through endocytosis, reducing synaptic communication. We planned to block the PICK1-GluA2 protein-protein interaction with a small molecule inhibitor to stabilize surface AMPA receptors as a therapeutic possibility for neurodegenerative diseases. Using a fluorescence polarization assay we identified compound BIO124 as a modest inhibitor of the PICK1-GluA2 interaction. We further tried to improve the binding affinity of BIO124 using structure-aided drug design but were unsuccessful in producing a co-crystal structure using previously reported crystallography methods for PICK1. Here we present a novel method through which we generated a co-crystal structure of the PDZ domain of PICK1 bound to BIO124. This article is protected by copyright. All rights reserved.


    Organizational Affiliation

    Biotherapeutics and Medicinal Sciences, Biogen Inc, Cambridge, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PRKCA-binding protein
A, B
125Homo sapiensMutation(s): 0 
Gene Names: PICK1 (PRKCABP)
Find proteins for Q9NRD5 (Homo sapiens)
Go to Gene View: PICK1
Go to UniProtKB:  Q9NRD5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 54.473α = 90.00
b = 54.473β = 90.00
c = 78.119γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-11-06 
  • Released Date: 2018-01-10 
  • Deposition Author(s): Marcotte, D.J.

Revision History 

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Structure summary
  • Version 1.2: 2018-02-28
    Type: Database references