Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.48 kDa 
• Atom Count: 3270 
• Residue Count: 379 
• Unique protein chains: 1

6FGY

Crystal Structure of Human BACE-1 in Complex with amino-1,4-oxazine compound 4

• DOI: 10.2210/pdb6FGY/pdb

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


• Deposited: 2018-01-11 Released: 2018-06-06 
• Deposition Author(s): Rondeau, J.-M., Bourgier, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.226 
• R-Value Work: 0.204 

Literature

Discovery of amino-1,4-oxazines as potent BACE-1 inhibitors.

Veenstra, S.J., Rueeger, H., Voegtle, M., Lueoend, R., Holzer, P., Hurth, K., Tintelnot-Blomley, M., Frederiksen, M., Rondeau, J.M., Jacobson, L., Staufenbiel, M., Neumann, U., Machauer, R.

(2018) Bioorg Med Chem Lett 28: 2195-2200

• PubMed: 29764741 
• DOI: 10.1016/j.bmcl.2018.05.003
• Primary Citation of Related Structures:  
  6FGY


• PubMed Abstract: 
  

New amino-1,4-oxazine derived BACE-1 inhibitors were explored and various synthetic routes developed. The binding mode of the inhibitors was elucidated by co-crystallization of 4 with BACE-1 and X-ray analysis. Subsequent optimization led to inhibitors with low double digit nanomolar activity in a biochemical and single digit nanomolar potency in a cellular assays. To assess the inhibitors for their permeation properties and potential to cross the blood-brain-barrier a MDR1-MDCK cell model was successfully applied. Compound 8a confirmed the in vitro results by dose-dependently reducing Aβ levels in mice in an acute treatment regimen.

---

Organizational Affiliation: 

Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	396	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817 GTEx  ENSG00000186318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D9W	A	~{N}-[3-[(3~{R})-5-azanyl-3-methyl-2,6-dihydro-1,4-oxazin-3-yl]phenyl]-5-bromanyl-pyridine-2-carboxamide C17 H17 Br N4 O2 HALWMQVNBCAXRZ-KRWDZBQOSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
D9W	IC50:  70   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.226 
• R-Value Work: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.056	α = 90
b = 76.738	β = 90
c = 104.214	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-01-11 
• Released Date: 2018-06-06 
Deposition Author(s): Rondeau, J.-M., Bourgier, E.

Revision History 

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection, Database references