4B1E | pdb_00004b1e

New Aminoimidazoles as BACE-1 Inhibitors: From Rational Design to Ab- lowering in Brain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.242 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4B1E

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

New aminoimidazoles as beta-secretase (BACE-1) inhibitors showing amyloid-beta (A beta ) lowering in brain.

Gravenfors, Y.Viklund, J.Blid, J.Ginman, T.Karlstrom, S.Kihlstrom, J.Kolmodin, K.Lindstrom, J.von Berg, S.von Kieseritzky, F.Bogar, K.Slivo, C.Swahn, B.M.Olsson, L.L.Johansson, P.Eketjall, S.Falting, J.Jeppsson, F.Stromberg, K.Janson, J.Rahm, F.

(2012) J Med Chem 55: 9297-9311

  • DOI: https://doi.org/10.1021/jm300991n
  • Primary Citation Related Structures: 
    4B1C, 4B1D, 4B1E

  • PubMed Abstract: 

    Amino-2H-imidazoles are described as a new class of BACE-1 inhibitors for the treatment of Alzheimer's disease. Synthetic methods, crystal structures, and structure-activity relationships for target activity, permeability, and hERG activity are reported and discussed. Compound (S)-1m was one of the most promising compounds in this report, with high potency in the cellular assay and a good overall profile. When guinea pigs were treated with compound (S)-1m, a concentration and time dependent decrease in Aβ40 and Aβ42 levels in plasma, brain, and CSF was observed. The maximum reduction of brain Aβ was 40-50%, 1.5 h after oral dosing (100 μmol/kg). The results presented highlight the potential of this new class of BACE-1 inhibitors with good target potency and with low effect on hERG, in combination with a fair CNS exposure in vivo.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, AstraZeneca R&D Södertälje, SE-151 85 Södertälje, Sweden. ylva.gravenfors@hotmail.com

Macromolecule Content 

  • Total Structure Weight: 43.53 kDa 
  • Atom Count: 3,215 
  • Modeled Residue Count: 375 
  • Deposited Residue Count: 388 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-SECRETASE 1388Homo sapiensMutation(s): 0 
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6T6

Query on 6T6



Download:Ideal Coordinates CCD File
B [auth A](2R)-2-methyl-5-phenyl-2-(3-pyridin-3-ylphenyl)-2,3-dihydro-1H-imidazol-4-amine
C21 H20 N4
BLSGQDNQCUBPGO-OAQYLSRUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.242 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.287α = 90
b = 75.074β = 90
c = 104.659γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references
  • Version 1.2: 2018-02-14
    Changes: Database references, Structure summary
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary