3L3A

Bace-1 with the aminopyridine Compound 32

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


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 acylguanidines have a high polar surface area (e ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A415Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
625
Query on 625
Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
625 Binding MOAD:  3L3A IC50: 420 (nM) from 1 assay(s)
BindingDB:  3L3A IC50: 420 (nM) from 1 assay(s)
PDBBind:  3L3A IC50: 420 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.227α = 90
b = 103.252β = 94.88
c = 49.784γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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