4BEK

CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH CHEMICAL LIGAND

• PDB DOI: https://doi.org/10.2210/pdb4BEK/pdb

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


• Deposited: 2013-03-11 Released: 2013-06-19 
• Deposition Author(s): Banner, D.W., Benz, J., Stihle, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.239 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Bace1 Inhibitors: A Head Group Scan on a Series of Amides.

Woltering, T.J., Wostl, W., Hilpert, H., Rogers-Evans, M., Pinard, E., Mayweg, A., Gobel, M., Banner, D.W., Benz, J., Travagli, M., Pollastrini, M., Marconi, G., Gabellieri, E., Guba, W., Mauser, H., Andreini, M., Jacobsen, H., Power, E., Narquizian, R.

(2013) Bioorg Med Chem Lett 23: 4239

• PubMed: 23735744 
• DOI: https://doi.org/10.1016/j.bmcl.2013.05.003
• Primary Citation of Related Structures:  
  4BEK, 4BFD


• PubMed Abstract: 
  

  A series of amides bearing a variety of amidine head groups was investigated as BACE1 inhibitors with respect to inhibitory activity in a BACE1 enzyme as well as a cell-based assay. Determination of their basicity as well as their properties as substrates of P-glycoprotein revealed that a 2-amino-1,3-oxazine head group would be a suitable starting point for further development of brain penetrating compounds for potential Alzheimer's disease treatment.

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Organizational Affiliation: 

F. Hoffmann-La Roche Ltd., Pharma Research, Grenzacherstr. 124, CH-4070 Basel, Switzerland. [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: 45.91 kDa 
• Atom Count: 3,071 
• Modelled Residue Count: 371 
• Deposited Residue Count: 409 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	409	Homo sapiens	Mutation(s): 1  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
XK0	B [auth A]	(4S)-4-(4-methoxyphenyl)-4-methyl-5,6-dihydro-1,3-thiazin-2-amine C12 H16 N2 O S VKHSIJFRPDEMHV-LBPRGKRZSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XK0	PDBBind:  4BEK	IC50: 4.12e+4 (nM) from 1 assay(s)
	BindingDB:  4BEK	IC50: min: 2630, max: 7.33e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.239 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.592	α = 90
b = 103.592	β = 90
c = 166.71	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Banner, D.W., Benz, J., Stihle, M.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.3: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description