6NCO

Fragment-based Discovery of an apoE4 Stabilizer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.707 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-Based Discovery of an Apolipoprotein E4 (apoE4) Stabilizer.

Petros, A.M.Korepanova, A.Jakob, C.G.Qiu, W.Panchal, S.C.Wang, J.Dietrich, J.D.Brewer, J.T.Pohlki, F.Kling, A.Wilcox, K.Lakics, V.Bahnassawy, L.Reinhardt, P.Partha, S.K.Bodelle, P.M.Lake, M.Charych, E.I.Stoll, V.S.Sun, C.Mohler, E.G.

(2019) J.Med.Chem. 62: 4120-4130

  • DOI: 10.1021/acs.jmedchem.9b00178
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Apolipoprotein E is a 299-residue lipid carrier protein produced in both the liver and the brain. The protein has three major isoforms denoted apoE2, apoE3, and apoE4 which differ at positions 112 and 158 and which occur at different frequencies in t ...

    Apolipoprotein E is a 299-residue lipid carrier protein produced in both the liver and the brain. The protein has three major isoforms denoted apoE2, apoE3, and apoE4 which differ at positions 112 and 158 and which occur at different frequencies in the human population. Genome-wide association studies indicate that the possession of two apoE4 alleles is a strong genetic risk factor for late-onset Alzheimer's disease (LOAD). In an attempt to identify a small molecule stabilizer of apoE4 function that may have utility as a therapy for Alzheimer's disease, we carried out an NMR-based fragment screen on the N-terminal domain of apoE4 and identified a benzyl amidine based fragment binder. In addition to NMR, binding was characterized using various other biophysical techniques, and a crystal structure of the bound core was obtained. Core elaboration ultimately yielded a compound that showed activity in an IL-6 and IL-8 cytokine release assay.


    Organizational Affiliation

    Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States.,Neuroscience Research , AbbVie Deutschland GmbH & Co. KG , Knollstrasse , 67061 Ludwigshafen , Germany.,AbbVie Neuroscience Research , 200 Sydney Street , Cambridge , Massachusetts 02139 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apolipoprotein E
A
185Homo sapiensMutation(s): 0 
Gene Names: APOE
Find proteins for P02649 (Homo sapiens)
Go to Gene View: APOE
Go to UniProtKB:  P02649
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KQP
Query on KQP

Download SDF File 
Download CCD File 
A
1-[5-chloro-4'-(2-hydroxypropan-2-yl)[1,1'-biphenyl]-3-yl]cyclobutane-1-carboximidamide
C20 H23 Cl N2 O
VORBWTOFIFETCY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.707 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.960α = 90.00
b = 52.870β = 90.00
c = 86.440γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
AutoPROCdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-12-11 
  • Released Date: 2019-04-17 
  • Deposition Author(s): Jakob, C.G., Qiu, W.

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references