6BJO

PICK1 PDZ domain in complex with the small molecule inhibitor BIO124.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1002/pro.3361
  • Primary Citation of Related Structures:  
    6BJN, 6BJO

  • 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 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.


  • Organizational Affiliation

    Neurodegeneration and Repair, Biogen Inc, Cambridge, Massachusetts.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PRKCA-binding protein
A, B
125Homo sapiensMutation(s): 0 
Gene Names: PICK1PRKCABP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRD5 (Homo sapiens)
Explore Q9NRD5 
Go to UniProtKB:  Q9NRD5
GTEx:  ENSG00000100151 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRD5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUY
Query on DUY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2S)-({4-(4-bromophenyl)-1-[1-(tert-butoxycarbonyl)-L-prolyl]piperidine-4-carbonyl}amino)(cyclopentyl)acetic acid
C29 H40 Br N3 O6
CZJLHKGARYEGAY-GOTSBHOMSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DUY Binding MOAD:  6BJO IC50: 513 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.011α = 90
b = 54.011β = 90
c = 77.873γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references