6NCO

Fragment-based Discovery of an apoE4 Stabilizer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apolipoprotein EA185Homo sapiensMutation(s): 1 
Gene Names: APOE
UniProt & NIH Common Fund Data Resources
Find proteins for P02649 (Homo sapiens)
Explore P02649 
Go to UniProtKB:  P02649
PHAROS:  P02649
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02649
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KQP (Subject of Investigation/LOI)
Query on KQP
Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
KQP Binding MOAD:  6NCO Kd: 3.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.96α = 90
b = 52.87β = 90
c = 86.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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