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: 46.73 kDa 
• Atom Count: 3004 
• Modelled Residue Count: 369 
• Deposited Residue Count: 415 
• Unique protein chains: 1

3IGB

Bace-1 with Compound 3

• PDB DOI: 10.2210/pdb3IGB/pdb

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


• Deposited: 2009-07-27 Released: 2009-11-03 
• Deposition Author(s): Olland, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.247 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Aminoimidazoles as potent and selective human beta-secretase (BACE1) inhibitors

Malamas, M.S., Erdei, J., Gunawan, I., Barnes, K., Johnson, M., Hui, Y., Turner, J., Hu, Y., Wagner, E., Fan, K., Olland, A., Bard, J., Robichaud, A.J.

(2009) J Med Chem 52: 6314-6323

• PubMed: 19757823 
• DOI: 10.1021/jm9006752
• Primary Citation of Related Structures:  
  3IGB


• PubMed Abstract: 
  

The identification of small molecule aminoimidazoles as potent and selective human beta-secretase inhibitors is reported. These analogues demonstrate low nannomolar potency for BACE1 in a FRET assay, exhibit comparable activity in a cell-based (ELISA) assay, and show >100x selectivity for the other structurally related aspartyl proteases BACE2, cathepsin D, renin, and pepsin. Our design strategy was supported by molecular modeling studies based on the cocrystal structure of the HTS-hit 3 in the BACE1 active site. These strategies enabled us to integrate pyridine and pyrimidine groups on 3 extending deep into the S3 region of the BACE1 binding pocket and enhancing the ligand's potency. Compound (R)-37 displayed an IC50 value for BACE1 of 20 nM, cellular activity of 90 nM, and >100-fold selectivity over related aspartyl proteases. Acute oral administration of (R)-37 at 30 mg/kg resulted in a significant 71% reduction of plasma Abeta40 measured at the 6 h time point in a Tg2576 mouse model (p < 0.001).

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Organizational Affiliation: 

Department of Chemical Sciences, Wyeth Research, CN 8000, Princeton, New Jersey 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
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
454	B [auth A]	8,8-diphenyl-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine C18 H18 N4 UFWSJOVQEPTPNE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
454	PDBBind:  3IGB	IC50: 3.80e+4 (nM) from 1 assay(s)
	BindingDB:  3IGB	IC50: min: 2.70e+4, max: 3.80e+4 (nM) from 2 assay(s)
		EC50: 1.60e+4 (nM) from 1 assay(s)
	Binding MOAD:  3IGB	IC50: 3.80e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.247 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.137	α = 90
b = 104.33	β = 94.69
c = 49.551	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-27 
• Released Date: 2009-11-03 
Deposition Author(s): Olland, A.M.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance