Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 46789.40 
• Atom Count: 2928 
• Residue Count: 415 
• Unique protein chains: 1

3S7M

Pyrazolyl and Thienyl Aminohydantoins as Potent BACE1 Inhibitors

• DOI: 10.2210/pdb3S7M/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2011-05-26 Released: 2011-08-31 
• Deposition Author(s): Chopra, R., Olland, A., Svenson, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.245 
• R-Value Work: 0.182 

Literature

New pyrazolyl and thienyl aminohydantoins as potent BACE1 inhibitors: Exploring the S2' region.

Malamas, M.S., Erdei, J., Gunawan, I., Barnes, K., Hui, Y., Johnson, M., Robichaud, A., Zhou, P., Yan, Y., Solvibile, W., Turner, J., Fan, K.Y., Chopra, R., Bard, J., Pangalos, M.N.

(2011) Bioorg.Med.Chem.Lett. 21: 5164-5170

• PubMed: 21835615 
• DOI: 10.1016/j.bmcl.2011.07.057
• Primary Citation of Related Structures:  
  3S7L


• PubMed Abstract: 
  

The proteolytic enzyme β-secretase (BACE1) plays a central role in the synthesis of the pathogenic β-amyloid in Alzheimer's disease. SAR studies of the S2' region of the BACE1 ligand binding pocket with pyrazolyl and thienyl P2' side chains are reported. These analogs exhibit low nanomolar potency for BACE1, and demonstrate >50- to 100-fold selectivity for the structurally related aspartyl proteases BACE2 and cathepsin D. Small groups attached at the nitrogen of the P2' pyrazolyl moiety, together with the P3 pyrimidine nucleus projecting into the S3 region of the binding pocket, are critical components to ligand's potency and selectivity. P2' thiophene side chain analogs are highly potent BACE1 inhibitors with excellent selectivity against cathepsin D, but only modest selectivity against BACE2. The cell-based activity of these new analogs tracked well with their increased molecular binding with EC(50) values of 0.07-0.2 μM in the ELISA assay for the most potent analogs.

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Organizational Affiliation: 

Pfizer Neuroscience Princeton, 865 Ridge Road, Monmouth Junction, NJ 08852, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Beta-secretase 1	A	415	Homo sapiens	Mutation(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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
532	A	(5S)-2-amino-3-methyl-5-[3-(pyridin-3-yl)phenyl]-5-(thiophen-3-yl)-3,5-dihydro-4H-imidazol-4-one WAY-253284 C19 H16 N4 O S AOGBXAFIKRFUPJ-IBGZPJMESA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
532	EC50: 420 nM (100) BINDINGDB
532	IC50: 60 nM (100) BINDINGDB
532	IC50: 60 nM BINDINGMOAD
532	IC50: 10 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.245 
• R-Value Work: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 72.389	α = 90.00
b = 103.979	β = 94.90
c = 50.137	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing
CrystalClear	data collection
HKL-2000	data reduction
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-26 
• Released Date: 2011-08-31 
• Deposition Author(s): Chopra, R., Olland, A., Svenson, K.

Revision History 

• Version 1.0: 2011-08-31
  Type: Initial release