3MSK

Fragment Based Discovery and Optimisation of BACE-1 Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
408Homo sapiensMutation(s): 0 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EV4
Query on EV4

Download SDF File 
Download CCD File 
A
4-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-cyclohexyl-N-methylbutanamide
C18 H25 Cl N4 O
UIWHCBCBZBYNDS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EV4IC50: 26000 nM (100) BINDINGDB
EV4IC50: 26000 nM BINDINGMOAD
EV4IC50: 26000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.510α = 90.00
b = 102.510β = 90.00
c = 170.528γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
DNAdata collection
MOSFLMdata reduction
REFMACrefinement
SCALAdata 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
  • Version 1.2: 2018-01-24
    Type: Advisory, Structure summary