2WEZ | pdb_00002wez

Human BACE-1 in complex with 1-ethyl-N-((1S,2R)-2-hydroxy-3-(((3-(methyloxy)phenyl)methyl)amino)-1-(phenylmethyl)propyl)-4-(2-oxo-1- pyrrolidinyl)-1H-indole-6-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.223 (Depositor) 
  • R-Value Work: 
    0.200 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2WEZ

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Second Generation of Bace-1 Inhibitors. Part 1: The Need for Improved Pharmacokinetics.

Charrier, N.Clarke, B.Cutler, L.Demont, E.Dingwall, C.Dunsdon, R.Hawkins, J.Howes, C.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: 3664

  • DOI: https://doi.org/10.1016/j.bmcl.2009.03.165
  • Primary Citation Related Structures: 
    2WEZ, 2WF0

  • PubMed Abstract: 

    Inhibition of the aspartyl protease BACE-1 has the potential to deliver a disease-modifying therapy for Alzheimer's disease. We have recently disclosed a series of transition-state mimetic BACE-1 inhibitors showing nanomolar potency in cell-based assays. Amongst them, GSK188909 (compound 2) had favorable pharmacokinetics and was the first orally bioavailable inhibitor reported to demonstrate brain amyloid lowering in an animal model. In this Letter, we describe the reasons that led us to favor a second generation of inhibitors for further in vivo studies.


  • 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: 44.32 kDa 
  • Atom Count: 3,438 
  • Modeled Residue Count: 373 
  • 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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZYE

Query on ZYE



Download:Ideal Coordinates CCD File
B [auth A]N-{(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}-1-ETHYL-4-(2-OXOPYRROLIDIN-1-YL)-1H-INDOLE-6-CARBOXAMIDE
C33 H38 N4 O4
BARAICYUEPEIRD-QCENPCRXSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.223 (Depositor) 
  • R-Value Work:  0.200 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.531α = 90
b = 76.758β = 90
c = 104.43γ = 90
Software Package:
Software NamePurpose
CNSrefinement

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: 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
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary