4B1D

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

• PDB DOI:  https://doi.org/10.2210/pdb4B1D/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-10 Released: 2012-10-10 
• Deposition Author(s): Rahm, F., Blid, J., Ginman, T., Karlstrom, S., Kihlstrom, J., Kolmodin, K., Lindstrom, J., von Berg, S., von Kieseritzky, F., Slivo, C., Swahn, B., Viklund, J., Olsson, L., Johansson, P., Eketjall, S., Falting, J., Jeppsson, F., Stromberg, K., Janson, J., Gravenfors, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.225 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

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

• PubMed: 23017051 
• DOI: https://doi.org/10.1021/jm300991n
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.7 kDa 
• Atom Count: 3,286 
• Modelled Residue Count: 376 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	388	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE, KIAA1149 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6TG	D [auth A]	(2S)-2-(4-methoxy-3,5-dimethylphenyl)-5-methyl-2-(3-pyrimidin-5-ylphenyl)-2H-imidazol-4-amine C23 H23 N5 O PZSMDBYYYKPYFV-QHCPKHFHSA-N
ACT	B [auth A], C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
6TG	BindingDB:  4B1D	IC50: min: 12, max: 49 (nM) from 4 assay(s)
	PDBBind:  4B1D	IC50: 32 (nM) from 1 assay(s)
	Binding MOAD:  4B1D	IC50: 12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.225 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.806	α = 90
b = 75.915	β = 90
c = 104.533	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Rahm, F., Blid, J., Ginman, T., Karlstrom, S., Kihlstrom, J., Kolmodin, K., Lindstrom, J., von Berg, S., von Kieseritzky, F., Slivo, C., Swahn, B., Viklund, J., Olsson, L., Johansson, P., Eketjall, S., Falting, J., Jeppsson, F., Stromberg, K., Janson, J., Gravenfors, Y.

Revision History  

• 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