3L3A

Bace-1 with the aminopyridine Compound 32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.362 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel pyrrolyl 2-aminopyridines as potent and selective human beta-secretase (BACE1) inhibitors.

Malamas, M.S.Barnes, K.Hui, Y.Johnson, M.Lovering, F.Condon, J.Fobare, W.Solvibile, W.Turner, J.Hu, Y.Manas, E.S.Fan, K.Olland, A.Chopra, R.Bard, J.Pangalos, M.N.Reinhart, P.Robichaud, A.J.

(2010) Bioorg.Med.Chem.Lett. 20: 2068-2073

  • DOI: 10.1016/j.bmcl.2010.02.075
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The proteolytic enzyme beta-secretase (BACE1) plays a central role in the synthesis of the pathogenic beta-amyloid in Alzheimer's disease. Recently, we reported small molecule acylguanidines as potent BACE1 inhibitors. However, many of these acylguan ...

    The proteolytic enzyme beta-secretase (BACE1) plays a central role in the synthesis of the pathogenic beta-amyloid in Alzheimer's disease. Recently, we reported small molecule acylguanidines as potent BACE1 inhibitors. However, many of these acylguanidines have a high polar surface area (e.g. as measured by the topological polar surface area or TPSA), which is unfavorable for crossing the blood-brain barrier. Herein, we describe the identification of the 2-aminopyridine moiety as a bioisosteric replacement of the acylguanidine moiety, which resulted in inhibitors with lower TPSA values and superior brain penetration. X-ray crystallographic studies indicated that the 2-aminopyridine moiety interacts directly with the catalytic aspartic acids Asp32 and Asp228 via a hydrogen-bonding network.


    Organizational Affiliation

    Department of Chemical Sciences, Wyeth, CN 8000, Princeton, NJ 08543-8000, USA. malamas.michael@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
415Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
625
Query on 625

Download SDF File 
Download CCD File 
A
4-(4-{1-[(6-aminopyridin-2-yl)methyl]-5-(2-chlorophenyl)-1H-pyrrol-2-yl}phenoxy)butanenitrile
C26 H23 Cl N4 O
CERJQPWNRISSQS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
625IC50: 420 nM (100) BINDINGDB
625IC50: 420 nM BINDINGMOAD
625IC50: 420 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.362 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.227α = 90.00
b = 103.252β = 94.88
c = 49.784γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data collection
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance