Fragment-based Discovery of an apoE4 Stabilizer

Experimental Data Snapshot

  • Resolution: 1.82 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/acs.jmedchem.9b00178
  • Primary Citation of Related Structures:  
    6NCN, 6NCO

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein E185Homo sapiensMutation(s): 1 
Gene Names: APOE
UniProt & NIH Common Fund Data Resources
Find proteins for P02649 (Homo sapiens)
Explore P02649 
Go to UniProtKB:  P02649
GTEx:  ENSG00000130203 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02649
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KJM (Subject of Investigation/LOI)
Query on KJM

Download Ideal Coordinates CCD File 
B [auth A]1-(3-chlorophenyl)cyclobutane-1-carboximidamide
C11 H13 Cl N2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.82 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.07α = 90
b = 52.79β = 90
c = 84.54γ = 90
Software Package:
Software NamePurpose
autoPROCdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description