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: 45.77 kDa 
• Atom Count: 3602 
• Modelled Residue Count: 394 
• Deposited Residue Count: 404 
• Unique protein chains: 1

4FM7

Crystal Structure of BACE with Compound 14g

• PDB DOI: 10.2210/pdb4FM7/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-15 Released: 2012-10-03 
• Deposition Author(s): Vajdos, F.F., Varghese, A.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.264 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

Spirocyclic sulfamides as beta-secretase 1 (BACE-1) inhibitors for the treatment of Alzheimer's disease: utilization of structure based drug design, WaterMap, and CNS penetration studies to identify centrally efficacious inhibitors.

Brodney, M.A., Barreiro, G., Ogilvie, K., Hajos-Korcsok, E., Murray, J., Vajdos, F., Ambroise, C., Christoffersen, C., Fisher, K., Lanyon, L., Liu, J., Nolan, C.E., Withka, J.M., Borzilleri, K.A., Efremov, I., Oborski, C.E., Varghese, A., O'Neill, B.T.

(2012) J Med Chem 55: 9224-9239

• PubMed: 22984865 
• DOI: 10.1021/jm3009426
• Primary Citation of Related Structures:  
  4FM7, 4FM8


• PubMed Abstract: 
  

β-Secretase 1 (BACE-1) is an attractive therapeutic target for the treatment and prevention of Alzheimer's disease (AD). Herein, we describe the discovery of a novel class of BACE-1 inhibitors represented by sulfamide 14g, using a medicinal chemistry strategy to optimize central nervous system (CNS) penetration by minimizing hydrogen bond donors (HBDs) and reducing P-glycoprotein (P-gp) mediated efflux. We have also taken advantage of the combination of structure based drug design (SBDD) to guide the optimization of the sulfamide analogues and the in silico tool WaterMap to explain the observed SAR. Compound 14g is a potent inhibitor of BACE-1 with excellent permeability and a moderate P-gp liability. Administration of 14g to mice produced a significant, dose-dependent reduction in central Aβ(X-40) levels at a free drug exposure equivalent to the whole cell IC(50) (100 nM). Furthermore, studies of the P-gp knockout mouse provided evidence that efflux transporters affected the amount of Aβ lowering versus that observed in wild-type (WT) mouse at an equivalent dose.

---

Related Citations: 

• High yield expression of human BACE constructs in Eschericia coli for refolding, purification, and high resolution diffracting crystal forms.
  Tomasselli, A.G., Paddock, D.J., Emmons, T.L., Mildner, A.M., Leone, J.W., Lull, J.M., Cialdella, J.I., Prince, D.B., Fischer, H.D., Heinrikson, R.L., Benson, T.E.
  (2008) Protein Pept Lett 15: 131

---

Organizational Affiliation: 

Department of Neuroscience, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	404	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0UP	B [auth A]	4-{[(5R,7S)-1-(3-fluorophenyl)-3,7-dimethyl-2,2-dioxido-2-thia-1,3,8-triazaspiro[4.5]dec-8-yl]methyl}-2-(propan-2-yloxy)phenol C24 H32 F N3 O4 S UICGCQDWRACUBV-MHECFPHRSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0UP	PDBBind:  4FM7	IC50: 100 (nM) from 1 assay(s)
	BindingDB:  4FM7	IC50: 100 (nM) from 1 assay(s)
	Binding MOAD:  4FM7	IC50: 100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.264 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.471	α = 90
b = 103.905	β = 90
c = 100.682	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-15 
• Released Date: 2012-10-03 
Deposition Author(s): Vajdos, F.F., Varghese, A.H.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references