Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 46.84 kDa 
• Atom Count: 3011 
• Residue Count: 370 
• Unique protein chains: 1

3IN4

Bace1 with Compound 38

• DOI: 10.2210/pdb3IN4/pdb

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


• Deposited: 2009-08-11 Released: 2010-01-19 
• Deposition Author(s): Olland, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.262 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

Di-substituted pyridinyl aminohydantoins as potent and highly selective human beta-secretase (BACE1) inhibitors.

Malamas, M.S., Barnes, K., Johnson, M., Hui, Y., Zhou, P., Turner, J., Hu, Y., Wagner, E., Fan, K., Chopra, R., Olland, A., Bard, J., Pangalos, M., Reinhart, P., Robichaud, A.J.

(2010) Bioorg Med Chem 18: 630-639

• PubMed: 20045648 
• DOI: 10.1016/j.bmc.2009.12.007
• Primary Citation of Related Structures:  
  3IN3, 3IN4


• PubMed Abstract: 
  

The identification of highly selective small molecule di-substituted pyridinyl aminohydantoins as beta-secretase inhibitors is reported. The more potent and selective analogs demonstrate low nanomolar potency for the BACE1 enzyme as measured in a FRET assay, and exhibit comparable activity in a cell-based (ELISA) assay. In addition, these pyridine-aminohydantoins are highly selectivity (>500x) against the other structurally related aspartyl proteases BACE2, cathepsin D, pepsin and renin. Our design strategy followed a traditional SAR approach and was supported by molecular modeling studies based on the previously reported aminohydantoin 3a. We have taken advantage of the amino acid difference between the BACE1 and BACE2 at the S2' pocket (BACE1 Pro(70) changed to BACE2 Lys(86)) to build ligands with >500-fold selectivity against BACE2. The addition of large substituents on the targeted ligand at the vicinity of this aberration has generated a steric conflict between the ligand and these two proteins, thus impacting the ligand's affinity and selectivity. These ligands have also shown an exceptional selectivity against cathepsin D (>5000-fold) as well as the other aspartyl proteases mentioned. One of the more potent compounds (S)-39 displayed an IC(50) value for BACE1 of 10nM, and exhibited cellular activity with an EC(50) value of 130nM in the ELISA assay.

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Organizational Affiliation: 

Department of Chemical Sciences, Wyeth Research, CN 8000, Princeton, NJ 08543-8000, 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
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817 GTEx  ENSG00000186318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BX2	A	(5S)-2-amino-5-(2,6-diethylpyridin-4-yl)-3-methyl-5-(3-pyrimidin-5-ylphenyl)-3,5-dihydro-4H-imidazol-4-one C23 H24 N6 O QQPRKWVAAAEILV-QHCPKHFHSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BX2	IC50:  30   nM  BindingDB
BX2	IC50:  40   nM  Binding MOAD
BX2	IC50:  40   nM  BindingDB
BX2	IC50 :  30   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.262 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.379	α = 90
b = 104.854	β = 94.79
c = 50.531	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-11 
• Released Date: 2010-01-19 
Deposition Author(s): Olland, A.M.

Revision History 

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance