Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 46644.68 
• Atom Count: 2965 
• Residue Count: 411 
• Unique protein chains: 1

4FRI

Crystal structure of BACE1 in complex with biarylspiro aminooxazoline 6

• DOI: 10.2210/pdb4FRI/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2012-06-26 Released: 2012-09-12 
• Deposition Author(s): Whittington, D.A., Long, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.246 
• R-Value Work: 0.197 

Literature

Structure- and Property-Based Design of Aminooxazoline Xanthenes as Selective, Orally Efficacious, and CNS Penetrable BACE Inhibitors for the Treatment of Alzheimer's Disease.

Huang, H., La, D.S., Cheng, A.C., Whittington, D.A., Patel, V.F., Chen, K., Dineen, T.A., Epstein, O., Graceffa, R., Hickman, D., Kiang, Y.H., Louie, S., Luo, Y., Wahl, R.C., Wen, P.H., Wood, S., Fremeau, R.T.

(2012) J.Med.Chem. 55: 9156-9169

• PubMed: 22928914 
• DOI: 10.1021/jm300598e
• Primary Citation of Related Structures:  
  4FRK, 4FRJ


• PubMed Abstract: 
  

A structure- and property-based drug design approach was employed to identify aminooxazoline xanthenes as potent and selective human β-secretase inhibitors. These compounds exhibited good isolated enzyme, cell potency, and selectivity against the structurally related aspartyl protease cathepsin D. Our efforts resulted in the identification of a potent, orally bioavailable CNS penetrant compound that exhibited in vivo efficacy. A single oral dose of compound 11a resulted in a significant reduction of CNS Aβ40 in naive rats.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: BACE1 Go to UniProtKB:  P56817

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
DWA	A	(4R)-4-[3-(2-fluoropyridin-3-yl)phenyl]-4-(4-methoxyphenyl)-4,5-dihydro-1,3-oxazol-2-amine C21 H18 F N3 O2 WCJQDRXUNINKDD-OAQYLSRUSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DWA	IC50: 2850 - 5100 nM (99) BINDINGDB
DWA	IC50: 2850 nM BINDINGMOAD
DWA	IC50: 2850 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.246 
• R-Value Work: 0.197 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 101.461	α = 90.00
b = 101.461	β = 90.00
c = 170.689	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-26 
• Released Date: 2012-09-12 
• Deposition Author(s): Whittington, D.A., Long, A.M.

Revision History 

• Version 1.0: 2012-09-12
  Type: Initial release
• Version 1.1: 2012-12-12
  Type: Database references