4X7I

Crystal Structure of BACE with amino thiazine inhibitor LY2886721

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

The Potent BACE1 Inhibitor LY2886721 Elicits Robust Central A beta Pharmacodynamic Responses in Mice, Dogs, and Humans.

May, P.C., Willis, B.A., Lowe, S.L., Dean, R.A., Monk, S.A., Cocke, P.J., Audia, J.E., Boggs, L.N., Borders, A.R., Brier, R.A., Calligaro, D.O., Day, T.A., Ereshefsky, L., Erickson, J.A., Gevorkyan, H., Gonzales, C.R., James, D.E., Jhee, S.S., Komjathy, S.F., Li, L., Lindstrom, T.D., Mathes, B.M., Martenyi, F., Sheehan, S.M., Stout, S.L., Timm, D.E., Vaught, G.M., Watson, B.M., Winneroski, L.L., Yang, Z., Mergott, D.J.

(2015) J Neurosci 35: 1199-1210

  • DOI: 10.1523/JNEUROSCI.4129-14.2015
  • Primary Citation of Related Structures:  
    4X7I

  • PubMed Abstract: 

    • BACE1 is a key protease controlling the formation of amyloid β, a peptide hypothesized to play a significant role in the pathogenesis of Alzheimer's disease (AD). Therefore, the development of potent and selective inhibitors of BACE1 has been a focus of many drug discovery efforts in academia and industry ...

    BACE1 is a key protease controlling the formation of amyloid β, a peptide hypothesized to play a significant role in the pathogenesis of Alzheimer's disease (AD). Therefore, the development of potent and selective inhibitors of BACE1 has been a focus of many drug discovery efforts in academia and industry. Herein, we report the nonclinical and early clinical development of LY2886721, a BACE1 active site inhibitor that reached phase 2 clinical trials in AD. LY2886721 has high selectivity against key off-target proteases, which efficiently translates in vitro activity into robust in vivo amyloid β lowering in nonclinical animal models. Similar potent and persistent amyloid β lowering was observed in plasma and lumbar CSF when single and multiple doses of LY2886721 were administered to healthy human subjects. Collectively, these data add support for BACE1 inhibition as an effective means of amyloid lowering and as an attractive target for potential disease modification therapy in AD.

    Organizational Affiliation: 

    Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, mergott_dustin_james@lilly.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B442Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3YS
Query on 3YS
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		N-{3-[(4aS,7aS)-2-amino-4a,5-dihydro-4H-furo[3,4-d][1,3]thiazin-7a(7H)-yl]-4-fluorophenyl}-5-fluoropyridine-2-carboxamide
C18 H16 F2 N4 O2 S
NIDRNVHMMDAAIK-YPMLDQLKSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3YS BindingDB:  4X7I IC50: min: 12, max: 20 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.432α = 90
b = 89.773β = 90
c = 130.663γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2014-12-09 
  • Released Date: 2014-12-24 
    • Deposition Author(s): Timm, D.E.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description, Source and taxonomy