1W51

BACE (Beta Secretase) in complex with a nanomolar non-peptidic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1W51/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-04 Released: 2004-09-23 
• Deposition Author(s): Patel, S., Vuillard, L., Cleasby, A., Murray, C.W., Yon, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.288 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

Apo and Inhibitor Complex Structures of Bace (Beta-Secretase)

Patel, S., Vuillard, L., Cleasby, A., Murray, C.W., Yon, J.

(2004) J Mol Biol 343: 407

• PubMed: 15451669 
• DOI: https://doi.org/10.1016/j.jmb.2004.08.018
• Primary Citation of Related Structures:  
  1W50, 1W51


• PubMed Abstract: 
  

  Human BACE, also known as beta-secretase, shows promise as a potential therapeutic target for Alzheimer's disease. We determined the apo structure of BACE to 1.75 A, and a structure of a hydroxyethylamine inhibitor complex derived by soaking. These show significant active-site movements compared to previously described BACE structures. Additionally, the structures reveal two pockets that could be targeted by structure-based drug design.

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Organizational Affiliation: 

Astex Technology, 436 Cambridge Science Park, Milton Road, CB4 0QA, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 46.86 kDa 
• Atom Count: 3,129 
• Modelled Residue Count: 375 
• 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): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L01	F [auth A]	3-[({(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}AMINO)(HYDROXY)METHYL]-N,N-DIPROPYLBENZAMIDE C32 H41 N3 O4 WPRACYICKOKGTO-XZWHSSHBSA-N
IOD	B [auth A], C [auth A], D [auth A], E [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
L01	PDBBind:  1W51	IC50: 500 (nM) from 1 assay(s)
	BindingDB:  1W51	IC50: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.288 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.351	α = 90
b = 102.351	β = 90
c = 168	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-23 
Deposition Author(s): Patel, S., Vuillard, L., Cleasby, A., Murray, C.W., Yon, J.

Revision History  

• Version 1.0: 2004-09-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary