4FRI

Crystal structure of BACE1 in complex with biarylspiro aminooxazoline 6

• PDB DOI: https://doi.org/10.2210/pdb4FRI/pdb

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


• 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: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

Starting Model: experimental

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: https://doi.org/10.1021/jm300598e
• Primary Citation of Related Structures:  
  4FRI, 4FRJ, 4FRK


• 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]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 46.64 kDa 
• Atom Count: 3,178 
• Modelled Residue Count: 372 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	411	Homo sapiens	Mutation(s): 2  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DWA	E [auth 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
IOD	B [auth A], C [auth A], D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DWA	BindingDB:  4FRI	IC50: min: 2850, max: 5100 (nM) from 2 assay(s)
	PDBBind:  4FRI	IC50: 2850 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.461	α = 90
b = 101.461	β = 90
c = 170.689	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary