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: 46.83 kDa 
• Atom Count: 3098 
• Modelled Residue Count: 367 
• Deposited Residue Count: 415 
• Unique protein chains: 1

3INF

Bace1 with the aminohydantoin Compound 37

• PDB DOI: 10.2210/pdb3INF/pdb

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


• Deposited: 2009-08-12 Released: 2010-03-02 
• Deposition Author(s): Olland, A.M., Chopra, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.231 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Design and synthesis of 5,5'-disubstituted aminohydantoins as potent and selective human beta-secretase (BACE1) inhibitors.

Malamas, M.S., Erdei, J., Gunawan, I., Turner, J., Hu, Y., Wagner, E., Fan, K., Chopra, R., Olland, A., Bard, J., Jacobsen, S., Magolda, R.L., Pangalos, M., Robichaud, A.J.

(2010) J Med Chem 53: 1146-1158

• PubMed: 19968289 
• DOI: 10.1021/jm901414e
• Primary Citation of Related Structures:  
  3IND, 3INE, 3INF, 3INH


• PubMed Abstract: 
  

The identification of small molecule aminohydantoins as potent and selective human beta-secretase inhibitors is reported. These analogues exhibit low nannomolar potency for BACE1, show comparable activity in a cell-based (ELISA) assay, and demonstrate >100x selectivity for the other structurally related aspartyl proteases BACE2, cathepsinD, renin, and pepsin. On the basis of the cocrystal structure of the HTS-hit 2 in the BACE1 active site and by use of a structure-based drug design approach, we methodically explored the comparatively large binding pocket of the BACE1 enzyme and identified key interactions between the ligand and the protein that contributed to the affinity. One of the more potent compounds, (S)-55, displayed an IC(50) value for BACE1 of 10 nM and exhibited comparable cellular activity (EC(50) = 20 nM) in the ELISA assay. Acute oral administration of (S)-55 at 100 mg/kg resulted in a 69% reduction of plasma A beta(40) at 8 h in a Tg2576 mouse (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
X45	B [auth A]	(5S)-2-amino-5-(4-methoxy-3-methylphenyl)-3-methyl-5-(3-pyridin-3-ylphenyl)-3,5-dihydro-4H-imidazol-4-one C23 H22 N4 O2 TWVGNKMRZLBNOD-QHCPKHFHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
X45	Binding MOAD:  3INF	IC50: 40 (nM) from 1 assay(s)
	BindingDB:  3INF	IC50: 40 (nM) from 1 assay(s)
		EC50: 120 (nM) from 1 assay(s)
	PDBBind:  3INF	IC50: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.231 
• R-Value Work: 0.194 
• 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
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-12 
• Released Date: 2010-03-02 
Deposition Author(s): Olland, A.M., Chopra, R.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance