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)

Macromolecule Content

• Total Structure Weight: 46.96 kDa 
• Atom Count: 3341 
• Residue Count: 363 
• Unique protein chains: 1

4XKX

Crystal structure of BACE1 in complex with 2-aminooxazoline 3-azaxanthene inhibitor 28

• DOI: 10.2210/pdb4XKX/pdb

• Classification: Hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-01-12 Released: 2015-02-04 
• Deposition Author(s): Whittington, D.A., Long, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Development of 2-aminooxazoline 3-azaxanthenes as orally efficacious beta-secretase inhibitors for the potential treatment of Alzheimer's disease.

Chen, J.J., Liu, Q., Yuan, C., Gore, V., Lopez, P., Ma, V., Amegadzie, A., Qian, W., Judd, T.C., Minatti, A.E., Brown, J., Cheng, Y., Xue, M., Zhong, W., Dineen, T.A., Epstein, O., Human, J., Kreiman, C., Marx, I., Weiss, M.M., Hitchcock, S.A., Powers, T.S., Chen, K., Wen, P.H., Whittington, D.A., Cheng, A.C., Bartberger, M.D., Hickman, D., Werner, J.A., Vargas, H.M., Everds, N.E., Vonderfecht, S.L., Dunn, R.T., Wood, S., Fremeau, R.T., White, R.D., Patel, V.F.

(2015) Bioorg Med Chem Lett 25: 767-774

• PubMed: 25613679 
• DOI: 10.1016/j.bmcl.2014.12.092
• Primary Citation of Related Structures:  
  4XKX


• PubMed Abstract: 
  

The β-site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1) is one of the most hotly pursued targets for the treatment of Alzheimer's disease. We used a structure- and property-based drug design approach to identify 2-aminooxazoline 3-azaxanthenes as potent BACE1 inhibitors which significantly reduced CSF and brain Aβ levels in a rat pharmacodynamic model. Compared to the initial lead 2, compound 28 exhibited reduced potential for QTc prolongation in a non-human primate cardiovascular safety model.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	411	Homo sapiens	Mutation(s): 2  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
43K	A	(5S)-7-(2-fluoropyridin-3-yl)-3-(2-fluoropyridin-4-yl)spiro[chromeno[2,3-c]pyridine-5,4'-[1,3]oxazol]-2'-amine C24 H15 F2 N5 O2 LEFDLEYZSDTVMO-DEOSSOPVSA-N
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
43K	IC50:  21   nM  BindingDB
43K	IC50:  0.8999999761581421   nM  Binding MOAD
43K	IC50:  0.8999999761581421   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.148	α = 90
b = 102.148	β = 90
c = 170.894	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-12 
• Released Date: 2015-02-04 
Deposition Author(s): Whittington, D.A., Long, A.M.

Revision History 

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2015-02-18
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description, Source and taxonomy