Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.62 kDa 
• Atom Count: 3245 
• Residue Count: 369 
• Unique protein chains: 1

4ZPE

BACE1 in complex with 4-(cyclohexylamino)-1-(3-fluorophenyl)-8-(3-isopropoxybenzyl)-1,3,8-triazaspiro[4.5]dec-3-en-2-one

• DOI: 10.2210/pdb4ZPE/pdb

• Classification: Hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-07 Released: 2015-08-05 
• Deposition Author(s): Orth, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Methyl-substitution of an iminohydantoin spiropiperidine beta-secretase (BACE-1) inhibitor has a profound effect on its potency.

Egbertson, M., McGaughey, G.B., Pitzenberger, S.M., Stauffer, S.R., Coburn, C.A., Stachel, S.J., Yang, W., Barrow, J.C., Neilson, L.A., McWherter, M., Perlow, D., Fahr, B., Munshi, S., Allison, T.J., Holloway, K., Selnick, H.G., Yang, Z., Swestock, J., Simon, A.J., Sankaranarayanan, S., Colussi, D., Tugusheva, K., Lai, M.T., Pietrak, B., Haugabook, S., Jin, L., Chen, I.W., Holahan, M., Stranieri-Michener, M., Cook, J.J., Vacca, J., Graham, S.L.

(2015) Bioorg Med Chem Lett 25: 4812-4819

• PubMed: 26195137 
• DOI: 10.1016/j.bmcl.2015.06.082
• Primary Citation of Related Structures:  
  4ZPE, 4ZPF, 4ZPG


• PubMed Abstract: 
  

The IC50 of a beta-secretase (BACE-1) lead compound was improved ∼200-fold from 11 μM to 55 nM through the addition of a single methyl group. Computational chemistry, small molecule NMR, and protein crystallography capabilities were used to compare the solution conformation of the ligand under varying pH conditions to its conformation when bound in the active site. Chemical modification then explored available binding pockets adjacent to the ligand. A strategically placed methyl group not only maintained the required pKa of the piperidine nitrogen and filled a small hydrophobic pocket, but more importantly, stabilized the conformation best suited for optimized binding to the receptor.

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Organizational Affiliation: 

Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	405	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
4QA	A	4-(cyclohexylamino)-1-(3-fluorophenyl)-8-[3-(propan-2-yloxy)benzyl]-1,3,8-triazaspiro[4.5]dec-3-en-2-one C29 H37 F N4 O2 KZMSAJWZLCSCQP-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4QA	IC50:  450   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.124	α = 90
b = 127.997	β = 90
c = 76.738	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-05-07 
• Released Date: 2015-08-05 
Deposition Author(s): Orth, P.

Revision History 

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references