3QBH

Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3QBH/pdb

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


• Deposited: 2011-01-13 Released: 2011-03-23 
• Deposition Author(s): Rondeau, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.219 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors.

Rueeger, H., Rondeau, J.M., McCarthy, C., Mobitz, H., Tintelnot-Blomley, M., Neumann, U., Desrayaud, S.

(2011) Bioorg Med Chem Lett 21: 1942-1947

• PubMed: 21388807 
• DOI: https://doi.org/10.1016/j.bmcl.2011.02.038
• Primary Citation of Related Structures:  
  3PI5, 3QBH


• PubMed Abstract: 
  

  This Letter describes the de novo design of non-peptidic hydroxyethylamine (HEA) inhibitors of BACE-1 by elimination of P-gp contributing amide attachments. The predicted binding mode of the novel cyclic sulfone HEA core template was confirmed in a X-ray co-crystal structure. Inhibitors of sub-micromolar potency with an improved property profile over historic HEA inhibitors resulting in improved brain penetration are described.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, Novartis Pharma AG, PO Box, CH-4002 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: 135.97 kDa 
• Atom Count: 9,482 
• Modelled Residue Count: 1,126 
• 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
QBH	D [auth A], E [auth B], F [auth C]	(4S)-4-(2-hydroxy-5-{[(3S,4S,5R)-4-hydroxy-1,1-dioxido-5-{[3-(propan-2-yl)benzyl]amino}tetrahydro-2H-thiopyran-3-yl]methyl}benzyl)-3-propyl-1,3-oxazolidin-2-one C29 H40 N2 O6 S JYNDAPHZRSRSGI-KAHNYGAISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QBH	BindingDB:  3QBH	IC50: 150 (nM) from 1 assay(s)
	PDBBind:  3QBH	IC50: 150 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.219 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.003	α = 90
b = 103.062	β = 103.98
c = 100.904	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Rondeau, J.M.

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-03-01
  Changes: Other
• Version 1.3: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary