4B77

Aminoimidazoles as BACE-1 Inhibitors: From De Novo Design to Ab- lowering in Brain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Core Refinement Toward Permeable Beta-Secretase (Bace-1) Inhibitors with Low Herg Activity.

Ginman, T., Viklund, J., Malmstrom, J., Blid, J., Emond, R., Forsblom, R., Johansson, A., Kers, A., Lake, F., Sehgelmeble, F., Sterky, K.J., Bergh, M., Lindgren, A., Johansson, P., Jeppsson, F., Falting, J., Gravenfors, Y., Rahm, F.

(2013) J Med Chem 56: 4181

  • DOI: 10.1021/jm3011349
  • Primary Citation of Related Structures:  
    4B72, 4B77, 4B78, 4B70

  • PubMed Abstract: 

    • By use of iterative design aided by predictive models for target affinity, brain permeability, and hERG activity, novel and diverse compounds based on cyclic amidine and guanidine cores were synthesized with the goal of finding BACE-1 inhibitors as a ...

    By use of iterative design aided by predictive models for target affinity, brain permeability, and hERG activity, novel and diverse compounds based on cyclic amidine and guanidine cores were synthesized with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. Since synthesis feasibility had low priority in the design of the cores, an extensive synthesis effort was needed to make the relevant compounds. Syntheses of these compounds are reported, together with physicochemical properties and structure-activity relationships based on in vitro data. Four crystal structures of diverse amidines binding in the active site are deposited and discussed. Inhibitors of BACE-1 with 3 μM to 32 nM potencies in cells are shown, together with data on in vivo brain exposure levels for four compounds. The results presented show the importance of the core structure for the profile of the final compounds.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85, Södertälje, Sweden.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-SECRETASE 1A388Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
GTEx  ENSG00000186318
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
54M
Query on 54M
Download Ideal Coordinates CCD File 
A
(5R)-5-(4-methoxyphenyl)-5-(3-pyrimidin-5-ylphenyl)-3,4-dihydropyrrol-2-amine
C21 H20 N4 O
MLDNPVIFXVSEGX-OAQYLSRUSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
54MIC50 :  7900   nM  PDBBind
54MIC50:  7900   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.885α = 90
b = 75.636β = 90
c = 104.613γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references