3FKT

Crystal Structure of Human Beta Secretase Complexed with Spiropiperdine Iminohydantoin Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3FKT/pdb
• Entry: 3FKT supersedes: 3E3W

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-12-17 Released: 2009-01-20 
• Deposition Author(s): Munshi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.217 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Discovery and X-ray Crystallographic Analysis of a Iminohydantoin Inhibitor of beta-Secretase

Barrow, J.C., Stauffer, S.R., Rittle, K.E., Ngo, P.L., Yang, M.S., Graham, S., McGaughey, G., Holloway, K., Tugusheva, S.K., Lai, M., Espeseth, A.S., Xu, M., Huang, Q., Zuck, P., Levorse, D.A., Hazuda, D., Vacca, J.P.

(2008) J Med Chem 51: 6259-6262

• PubMed: 18811140 
• DOI: https://doi.org/10.1021/jm800914n
• Primary Citation of Related Structures:  
  3FKT


• PubMed Abstract: 
  

  A high-throughput screen at 100 microM inhibitor concentration for the BACE-1 enzyme revealed a novel spiropiperidine iminohydantoin aspartyl protease inhibitor template. An X-ray cocrystal structure with BACE-1 revealed a novel mode of binding whereby the inhibitor interacts with the catalytic aspartates via bridging water molecules. Using the crystal structure as a guide, potent compounds with good brain penetration were designed.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.61 kDa 
• Atom Count: 3,273 
• Modelled Residue Count: 368 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	405	Homo sapiens	Mutation(s): 2  Gene Names: BACE, BACE1, 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
SII	B [auth A]	N-(4-{[4-(cyclohexylamino)-1-(3-fluorophenyl)-2-oxo-1,3,8-triazaspiro[4.5]dec-3-en-8-yl]methyl}phenyl)acetamide C28 H34 F N5 O2 VXIOVOURIXSOTD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SII	BindingDB:  3FKT	IC50: 2800 (nM) from 1 assay(s)
	PDBBind:  3FKT	IC50: 2800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.217 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.743	α = 90
b = 128.042	β = 90
c = 76.768	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Munshi, S.
• This entry supersedes: 3E3W

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary