3MSJ

Structure of bace (beta secretase) in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-based discovery and optimization of BACE1 inhibitors.

Madden, J.Dod, J.R.Godemann, R.Kraemer, J.Smith, M.Biniszkiewicz, M.Hallett, D.J.Barker, J.Dyekjaer, J.D.Hesterkamp, T.

(2010) Bioorg.Med.Chem.Lett. 20: 5329-5333

  • DOI: 10.1016/j.bmcl.2010.06.089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A novel series of 2-aminobenzimidazole inhibitors of BACE1 has been discovered using fragment-based drug discovery (FBDD) techniques. The rapid optimization of these inhibitors using structure-guided medicinal chemistry is discussed.

    A novel series of 2-aminobenzimidazole inhibitors of BACE1 has been discovered using fragment-based drug discovery (FBDD) techniques. The rapid optimization of these inhibitors using structure-guided medicinal chemistry is discussed.


    Organizational Affiliation

    Evotec UK Ltd, Abingdon, UK. james.madden@evotec.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-SECRETASE 1
A, B, C
411Homo sapiensMutation(s): 2 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EV3
Query on EV3

Download SDF File 
Download CCD File 
A, B, C
3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol
C10 H12 Cl N3 O
NSMVCZCLMLZSOB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EV3IC50: 770000 nM (99) BINDINGDB
EV3IC50: 770000 nM BINDINGMOAD
EV3IC50: 770000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 229.196α = 90.00
b = 98.829β = 103.36
c = 63.132γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance