2WF3 | pdb_00002wf3

Human BACE-1 in complex with 6-(ethylamino)-N-((1S,2R)-2-hydroxy-3-(((3-(methyloxy)phenyl)methyl)amino)-1-(phenylmethyl)propyl)-1-methyl-1, 3,4,5-tetrahydro-2,1-benzothiazepine-8-carboxamide 2,2-dioxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.217 (Depositor) 
  • R-Value Work: 
    0.164 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2WF3

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

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

  • DOI: https://doi.org/10.1016/j.bmcl.2009.03.150
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 44.71 kDa 
  • Atom Count: 3,345 
  • Modeled Residue Count: 375 
  • Deposited Residue Count: 392 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-SECRETASE 1392Homo sapiensMutation(s): 4 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.217 (Depositor) 
  • R-Value Work:  0.164 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.453α = 90
b = 76.868β = 90
c = 104.478γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary