Human BACE-1 in complex with 3-(1,1-dioxidotetrahydro-2H-1,2-thiazin- 2-yl)-5-(ethylamino)-N-((1S,2R)-2-hydroxy-1-(phenylmethyl)-3-(((3-(trifluoromethyl)phenyl)methyl)amino)propyl)benzamide

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Second Generation of Hydroxyethylamine Bace-1 Inhibitors: Optimizing Potency and Oral Bioavailability.

Charrier, N.Clarke, B.Cutler, L.Demont, E.Dingwall, C.Dunsdon, R.East, P.Hawkins, J.Howes, C.Hussain, I.Jeffrey, P.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.

(2008) J Med Chem 51: 3313

  • DOI: https://doi.org/10.1021/jm800138h
  • Primary Citation of Related Structures:  
    2VNM, 2VNN

  • PubMed Abstract: 

    BACE-1 inhibition has the potential to provide a disease-modifying therapy for the treatment of Alzheimer's disease. Optimization of a first generation of BACE-1 inhibitors led to the discovery of novel hydroxyethylamines (HEAs) bearing a tricyclic nonprime side. These derivatives have nanomolar cell potency and are orally bioavailable.

  • Organizational Affiliation

    Neurology and Gastrointestinal Centre of Excellence for Drug Discovery, GlaxoSmithKline, New Frontiers Park, Harlow, Essex, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-SECRETASE 1392Homo sapiensMutation(s): 4 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CM8

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C31 H37 F3 N4 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
CM8 BindingDB:  2VNM IC50: min: 3, max: 7 (nM) from 3 assay(s)
Binding MOAD:  2VNM IC50: 3 (nM) from 1 assay(s)
PDBBind:  2VNM IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.952α = 90
b = 76.217β = 90
c = 104.492γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-20
    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: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2019-05-15
    Changes: Data collection, Experimental preparation