Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 46.79 kDa 
• Atom Count: 3075 
• Modelled Residue Count: 371 
• Deposited Residue Count: 415 
• Unique protein chains: 1

3S7M

Pyrazolyl and Thienyl Aminohydantoins as Potent BACE1 Inhibitors

• PDB DOI: 10.2210/pdb3S7M/pdb

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


• 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: 2.20 Å
• R-Value Free: 0.245 
• R-Value Work: 0.182 
• R-Value Observed: 0.186 

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, 3S7M


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	415	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 GTEx:  ENSG00000186318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
532	B [auth A]	(5S)-2-amino-3-methyl-5-[3-(pyridin-3-yl)phenyl]-5-(thiophen-3-yl)-3,5-dihydro-4H-imidazol-4-one C19 H16 N4 O S AOGBXAFIKRFUPJ-IBGZPJMESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
532	PDBBind:  3S7M	IC50: 10 (nM) from 1 assay(s)
	Binding MOAD:  3S7M	IC50: 60 (nM) from 1 assay(s)
	BindingDB:  3S7M	IC50: 60 (nM) from 1 assay(s)
		EC50: 420 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.245 
• R-Value Work: 0.182 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.389	α = 90
b = 103.979	β = 94.9
c = 50.137	γ = 90

Software Package:

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

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