4ZSM

BACE crystal structure with bicyclic aminothiazine fragment

• PDB DOI:  https://doi.org/10.2210/pdb4ZSM/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-13 Released: 2015-06-10 
• Deposition Author(s): Timm, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.258 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Literature

Preparation and biological evaluation of conformationally constrained BACE1 inhibitors.

Winneroski, L.L., Schiffler, M.A., Erickson, J.A., May, P.C., Monk, S.A., Timm, D.E., Audia, J.E., Beck, J.P., Boggs, L.N., Borders, A.R., Boyer, R.D., Brier, R.A., Hudziak, K.J., Klimkowski, V.J., Garcia Losada, P., Mathes, B.M., Stout, S.L., Watson, B.M., Mergott, D.J.

(2015) Bioorg Med Chem 23: 3260-3268

• PubMed: 26001341 
• DOI: https://doi.org/10.1016/j.bmc.2015.04.062
• Primary Citation of Related Structures:  
  4ZSM, 4ZSP, 4ZSQ, 4ZSR


• PubMed Abstract: 
  

The BACE1 enzyme is a key target for Alzheimer's disease. During our BACE1 research efforts, fragment screening revealed that bicyclic thiazine 3 had low millimolar activity against BACE1. Analysis of the co-crystal structure of 3 suggested that potency could be increased through extension toward the S3 pocket and through conformational constraint of the thiazine core. Pursuit of S3-binding groups produced low micromolar inhibitor 6, which informed the S3-design for constrained analogs 7 and 8, themselves prepared via independent, multi-step synthetic routes. Biological characterization of BACE inhibitors 6-8 is described.

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Organizational Affiliation: 

Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, IN 46285, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.37 kDa 
• Atom Count: 6,633 
• Modelled Residue Count: 776 
• Deposited Residue Count: 884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	442	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4RW	C [auth A], E [auth B]	(4aS,8aR)-4a,5,6,7,8,8a-hexahydro-4H-3,1-benzothiazin-2-amine C8 H14 N2 S SZAFVQHJBWFBIQ-RNFRBKRXSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4RW	BindingDB:  4ZSM	IC50: 4.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.258 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.793	α = 90
b = 86.519	β = 97.62
c = 112.314	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Timm, D.E.

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2015-06-17
  Changes: Database references