3L38

Bace1 in complex with the aminopyridine Compound 44


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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:  
    3L38, 3L3A

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A415Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
879
Query on 879

Download CCD File 
A
6-({2-(2-chlorophenyl)-5-[4-(pyrimidin-5-yloxy)phenyl]-1H-pyrrol-1-yl}methyl)pyridin-2-amine
C26 H20 Cl N5 O
MNZJYJDKCYJKMU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
879IC50:  100   nM  BindingDB
879IC50:  100   nM  Binding MOAD
879IC50 :  100   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.253α = 90
b = 103.687β = 95.04
c = 49.983γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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