3S2O

Fragment based discovery and optimisation of bace-1 inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 

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 2 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
EV6
Query on EV6

Download SDF File 
Download CCD File 
A
(3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]pentanamide
C22 H29 Cl N4 O
KMAKOMVKNWTGPE-LIXZBVSLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EV6IC50: 8900 nM (100) BINDINGDB
EV6IC50: 8900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.880α = 90.00
b = 101.880β = 90.00
c = 170.181γ = 120.00
Software Package:
Software NamePurpose
DNAdata collection
REFMACrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-09-07
    Type: Structure summary