4LXM

Crystal Structure of Human Beta Secretase in Complex with compound 12a

• PDB DOI: https://doi.org/10.2210/pdb4LXM/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-30 Released: 2013-08-28 
• Deposition Author(s): Rondeau, J.M., Bourgier, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.218 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Discovery of cyclic sulfoxide hydroxyethylamines as potent and selective beta-site APP-cleaving enzyme 1 (BACE1) inhibitors: structure based design and in vivo reduction of amyloid beta-peptides.

Rueeger, H., Lueoend, R., Machauer, R., Veenstra, S.J., Jacobson, L.H., Staufenbiel, M., Desrayaud, S., Rondeau, J.M., Mobitz, H., Neumann, U.

(2013) Bioorg Med Chem Lett 23: 5300-5306

• PubMed: 23981898 
• DOI: https://doi.org/10.1016/j.bmcl.2013.07.071
• Primary Citation of Related Structures:  
  4LXA, 4LXK, 4LXM


• PubMed Abstract: 
  

  Previous structure based optimization in our laboratories led to the identification of a novel, high-affinity cyclic sulfone hydroxyethylamine-derived inhibitor such as 1 that lowers CNS-derived Aβ following oral administration to transgenic APP51/16 mice. Herein we report SAR development in the S3 and S2' subsites of BACE1 for cyclic sulfoxide hydroxyethyl amine inhibitors, the synthetic approaches employed in this effort, and in vivo data for optimized compound such as 11d.

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Organizational Affiliation: 

Department of Global Discovery Chemistry, Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 136.09 kDa 
• Atom Count: 9,581 
• Modelled Residue Count: 1,135 
• Deposited Residue Count: 1,206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	402	Homo sapiens	Mutation(s): 0  Gene Names: BACE, BACE1, 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1YU	D [auth A], E [auth B], F [auth C]	(1S,3S,4S,5R)-3-{4-amino-3-fluoro-5-[(1,1,1,3,3,3-hexafluoropropan-2-yl)oxy]benzyl}-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1-oxide C26 H31 F7 N2 O3 S SVZBUJIOBQPGEC-DAMLKHMOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1YU	PDBBind:  4LXM	IC50: 88 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.218 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.29	α = 90
b = 104.447	β = 104.3
c = 100.487	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Rondeau, J.M., Bourgier, E.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Other
• Version 1.2: 2013-11-20
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary