2WF1

Human BACE-1 in complex with 7-ethyl-N-((1S,2R)-2-hydroxy-3-(((3-(methyloxy)phenyl(methyl)amino)-1-(phenylmethyl)propyl)-1-methyl-3,4- dihydro-1H-(1,2,5)thiadiazepino(3,4,5-hi)indole-9-carboxamide 2,2- dioxide

• PDB DOI:  https://doi.org/10.2210/pdb2WF1/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2009-04-02 Released: 2009-05-19 
• Deposition Author(s): Charrier, N., Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Hubbard, J., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.207 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Second Generation of Bace-1 Inhibitors Part 2: Optimisation of the Non-Prime Side Substituent.

Charrier, N., Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Hubbard, J., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

(2009) Bioorg Med Chem Lett 19: 3669

• PubMed: 19477642 
• DOI: https://doi.org/10.1016/j.bmcl.2009.03.150
• Primary Citation of Related Structures:  
  2WF1, 2WF2, 2WF3


• PubMed Abstract: 
  

Our first generation of hydroxyethylamine transition-state mimetic BACE-1 inhibitors allowed us to validate BACE-1 as a key target for Alzheimer's disease by demonstrating amyloid lowering in an animal model, albeit at rather high doses. Finding a molecule from this series which was active at lower oral doses proved elusive and demonstrated the need to find a novel series of inhibitors with improved pharmacokinetics. This Letter describes the discovery of such inhibitors.

---

Organizational Affiliation: 

Neurology and Gastrointestinal Centre of Excellence for Drug Discovery, GlaxoSmithKline R&D, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, United Kingdom.

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: 44.35 kDa 
• Atom Count: 3,418 
• Modelled Residue Count: 375 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	392	Homo sapiens	Mutation(s): 4  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZY1	B [auth A]	N-{(1S,2R)-1-benzyl-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-7-ethyl-1-methyl-3,4-dihydro-1H-[1,2,5]thiadiazepino[3,4,5-hi]indole-9-carboxamide 2,2-dioxide C32 H38 N4 O5 S MNGUVHPNHVMEDL-MFMCTBQISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZY1	BindingDB:  2WF1	IC50: 2 (nM) from 1 assay(s)
	PDBBind:  2WF1	IC50: 2 (nM) from 1 assay(s)
	Binding MOAD:  2WF1	IC50: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.207 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.177	α = 90
b = 77.001	β = 90
c = 104.237	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Charrier, N., Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Hubbard, J., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

Revision History  

• Version 1.0: 2009-05-19
  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: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-15
  Changes: Data collection, Experimental preparation