Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | 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: 46.49 kDa 
• Atom Count: 3432 
• Modelled Residue Count: 375 
• Deposited Residue Count: 411 
• Unique protein chains: 1

4AZY

Design and Synthesis of BACE1 Inhibitors with In Vivo Brain Reduction of beta-Amyloid Peptides (COMPOUND 10)

• DOI: 10.2210/pdb4AZY/pdb

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


• Deposited: 2012-06-27 Released: 2012-10-17 
• Deposition Author(s): Swahn, B.M., Kolmodin, K., Karlstrom, S., von Berg, S., Soderman, P., Holenz, J., Berg, S., Lindstrom, J., Sundstrom, M., Turek, D., Kihlstrom, J., Slivo, C., Andersson, L., Pyring, D., Ohberg, L., Kers, A., Bogar, K., Bergh, M., Olsson, L.L., Janson, J., Eketjall, S., Georgievska, B., Jeppsson, F., Falting, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.210 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Design and synthesis of beta-site amyloid precursor protein cleaving enzyme (BACE1) inhibitors with in vivo brain reduction of beta-amyloid peptides.

Swahn, B.M., Kolmodin, K., Karlstrom, S., von Berg, S., Soderman, P., Holenz, J., Berg, S., Lindstrom, J., Sundstrom, M., Turek, D., Kihlstrom, J., Slivo, C., Andersson, L., Pyring, D., Rotticci, D., Ohberg, L., Kers, A., Bogar, K., von Kieseritzky, F., Bergh, M., Olsson, L.L., Janson, J., Eketjall, S., Georgievska, B., Jeppsson, F., Falting, J.

(2012) J Med Chem 55: 9346-9361

• PubMed: 22924815 
• DOI: 10.1021/jm3009025
• Primary Citation of Related Structures:  
  4AZY, 4B00


• PubMed Abstract: 
  

The evaluation of a series of aminoisoindoles as β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors and the discovery of a clinical candidate drug for Alzheimer's disease, (S)-32 (AZD3839), are described. The improvement in permeability properties by the introduction of fluorine adjacent to the amidine moiety, resulting in in vivo brain reduction of Aβ40, is discussed. Due to the basic nature of these compounds, they displayed affinity for the human ether-a-go-go related gene (hERG) ion channel. Different ways to reduce hERG inhibition and increase hERG margins for this series are described, culminating in (S)-16 and (R)-41 showing large in vitro margins with BACE1 cell IC(50) values of 8.6 and 0.16 nM, respectively, and hERG IC(50) values of 16 and 2.8 μM, respectively. Several compounds were advanced into pharmacodynamic studies and demonstrated significant reduction of β-amyloid peptides in mouse brain following oral dosing.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85, Södertälje, Sweden. [e-mail]

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
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
7F3 (Subject of Investigation/LOI)	F [auth A]	(1S)-4-fluoro-1-(4-fluoro-3-pyrimidin-5-ylphenyl)-1-[2-(trifluoromethyl)pyridin-4-yl]-1H-isoindol-3-amine C24 H14 F5 N5 UDQUVXUVXUGJFO-QHCPKHFHSA-N
ACT	B [auth A], C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7F3	BindingDB:  4AZY	IC50: min: 22, max: 204 (nM) from 5 assay(s)
	PDBBind:  4AZY	IC50: 198 (nM) from 1 assay(s)
	Binding MOAD:  4AZY	IC50: 125 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.210 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.54	α = 90
b = 76.39	β = 90
c = 104.34	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2012-06-27 
• Released Date: 2012-10-17 
Deposition Author(s): Swahn, B.M., Kolmodin, K., Karlstrom, S., von Berg, S., Soderman, P., Holenz, J., Berg, S., Lindstrom, J., Sundstrom, M., Turek, D., Kihlstrom, J., Slivo, C., Andersson, L., Pyring, D., Ohberg, L., Kers, A., Bogar, K., Bergh, M., Olsson, L.L., Janson, J., Eketjall, S., Georgievska, B., Jeppsson, F., Falting, J.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references
• Version 1.2: 2018-02-14
  Changes: Database references, Structure summary