6BFD

BACE crystal structure with hydroxy pyrrolidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Optimization of Hydroxyethylamine Transition State Isosteres as Aspartic Protease Inhibitors by Exploiting Conformational Preferences.

Bueno, A.B.Agejas, J.Broughton, H.Dally, R.Durham, T.B.Espinosa, J.F.Gonzalez, R.Hahn, P.J.Marcos, A.Rodriguez, R.Sanz, G.Soriano, J.F.Timm, D.Vidal, P.Yang, H.C.McCarthy, J.R.

(2017) J. Med. Chem. 60: 9807-9820

  • DOI: 10.1021/acs.jmedchem.7b01304
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NMR conformational analysis of a hydroxyethylamine peptide isostere developed as an aspartic protease inhibitor shows that it is a flexible architecture. Cyclization to form pyrrolidines, piperidines, or morpholines results in a preorganization of th ...

    NMR conformational analysis of a hydroxyethylamine peptide isostere developed as an aspartic protease inhibitor shows that it is a flexible architecture. Cyclization to form pyrrolidines, piperidines, or morpholines results in a preorganization of the whole system in solution. The resulting conformation is similar to the conformation of the inhibitor in the active site of BACE-1. This entropic gain results in increased affinity for the enzyme when compared with the acyclic system. For morpholines 27 and 29, the combination of steric and electronic factors is exploited to orient substituents toward S1, S1', and S2' pockets both in the solution and in the bound states. These highly preorganized molecules proved to be the most potent compounds of the series. Additionally, the morpholines, unlike the pyrrolidine and piperidine analogues, have been found to be brain penetrant BACE-1 inhibitors.


    Organizational Affiliation

    Lilly SA , Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain.,Lilly Research Laboratories , Indianapolis, Indiana 46285, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B
442Homo sapiensMutation(s): 0 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DJS
Query on DJS

Download SDF File 
Download CCD File 
A, B
2-{[(2S)-butan-2-yl]amino}-N-{(1R,2S)-1-hydroxy-3-phenyl-1-[(2R)-pyrrolidin-2-yl]propan-2-yl}-6-(methylsulfonyl)pyridine-4-carboxamide
C24 H34 N4 O4 S
CNZLAHITQXPOEJ-YLTWVVNKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DJSIC50: 5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.460α = 90.00
b = 89.410β = 90.00
c = 131.410γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
CNXphasing
SCALEITdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-10-26 
  • Released Date: 2017-11-15 
  • Deposition Author(s): Timm, D.E.

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references