4YBI

Crystal structure of BACE with amino thiazine inhibitor LY2811376

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


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Literature

Robust central reduction of amyloid-beta in humans with an orally available, non-peptidic beta-secretase inhibitor.

May, P.C., Dean, R.A., Lowe, S.L., Martenyi, F., Sheehan, S.M., Boggs, L.N., Monk, S.A., Mathes, B.M., Mergott, D.J., Watson, B.M., Stout, S.L., Timm, D.E., Smith Labell, E., Gonzales, C.R., Nakano, M., Jhee, S.S., Yen, M., Ereshefsky, L., Lindstrom, T.D., Calligaro, D.O., Cocke, P.J., Greg Hall, D., Friedrich, S., Citron, M., Audia, J.E.

(2011) J Neurosci 31: 16507-16516

  • DOI: 10.1523/JNEUROSCI.3647-11.2011
  • Primary Citation of Related Structures:  
    4YBI

  • PubMed Abstract: 

    • According to the amyloid cascade hypothesis, cerebral deposition of amyloid-β peptide (Aβ) is critical for Alzheimer's disease (AD) pathogenesis. Aβ generation is initiated when β-secretase (BACE1) cleaves the amyloid precursor protein. For more than a decade, BACE1 has been a prime target for designing drugs to prevent or treat AD ...

    According to the amyloid cascade hypothesis, cerebral deposition of amyloid-β peptide (Aβ) is critical for Alzheimer's disease (AD) pathogenesis. Aβ generation is initiated when β-secretase (BACE1) cleaves the amyloid precursor protein. For more than a decade, BACE1 has been a prime target for designing drugs to prevent or treat AD. However, development of such agents has turned out to be extremely challenging, with major hurdles in cell penetration, oral bioavailability/metabolic clearance, and brain access. Using a fragment-based chemistry strategy, we have generated LY2811376 [(S)-4-(2,4-difluoro-5-pyrimidin-5-yl-phenyl)-4-methyl-5,6-dihydro-4H-[1,3]thiazin-2-ylamine], the first orally available non-peptidic BACE1 inhibitor that produces profound Aβ-lowering effects in animals. The biomarker changes obtained in preclinical animal models translate into man at doses of LY2811376 that were safe and well tolerated in healthy volunteers. Prominent and long-lasting Aβ reductions in lumbar CSF were measured after oral dosing of 30 or 90 mg of LY2811376. This represents the first translation of BACE1-driven biomarker changes in CNS from preclinical animal models to man. Because of toxicology findings identified in longer-term preclinical studies, this compound is no longer progressing in clinical development. However, BACE1 remains a viable target because the adverse effects reported here were recapitulated in LY2811376-treated BACE1 KO mice and thus are unrelated to BACE1 inhibition. The magnitude and duration of central Aβ reduction obtainable with BACE1 inhibition positions this protease as a tractable small-molecule target through which to test the amyloid hypothesis in man.

    Organizational Affiliation: 

    Lilly Research Laboratories, Eli Lilly & Co., Indianapolis, Indiana 46285, USA.



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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4B2
Query on 4B2
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		(4S)-4-[2,4-difluoro-5-(pyrimidin-5-yl)phenyl]-4-methyl-5,6-dihydro-4H-1,3-thiazin-2-amine
C15 H14 F2 N4 S
MJQMRGWYPNIERM-HNNXBMFYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B],
H [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4B2 BindingDB:  4YBI IC50: min: 173, max: 620 (nM) from 7 assay(s)
EC50: 300 (nM) from 1 assay(s)
Binding MOAD:  4YBI IC50: 239 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.768α = 90
b = 90.786β = 90
c = 131.753γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2015-02-18 
  • Released Date: 2015-04-01 
    • Deposition Author(s): Timm, D.E.

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release