2XFI

Human BACE-1 in complex with N-((1S,2R)-3-(((1S)-2-(cyclohexylamino)- 1-methyl-2-oxoethyl)amino)-2-hydroxy-1-(phenylmethyl)propyl)-3-((methylsulfonyl)(phenyl)amino)benzamide

• PDB DOI: https://doi.org/10.2210/pdb2XFI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2010-05-24 Released: 2010-07-07 
• Deposition Author(s): Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Howes, C., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.198 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Literature

Bace-1 Inhibitors Using Novel Edge-to-Face Interaction with Arg-296

Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Howes, C., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

(2010) Bioorg Med Chem Lett 20: 4639

• PubMed: 20579874 
• DOI: https://doi.org/10.1016/j.bmcl.2010.05.111
• Primary Citation of Related Structures:  
  2XFI, 2XFJ, 2XFK


• PubMed Abstract: 
  

  Inhibition of the aspartyl protease BACE-1 has the potential to deliver a disease-modifying therapy for Alzheimer's disease. Herein, is described a series of potent inhibitors based on an hydroxyethylamine (HEA) transition state mimetic template. These inhibitors interact with the non prime side of the enzyme using a novel edge-to-face interaction with Arg-296.

---

Organizational Affiliation: 

Neurology and Gastrointestinal Centre of Excellence for Drug Discovery, GlaxoSmithKline R&D, New Frontiers Science Park, Harlow, Essex, UK.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.37 kDa 
• Atom Count: 3,460 
• Modelled Residue Count: 373 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	392	Homo sapiens	Mutation(s): 4  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
XFI	B [auth A]	N-((1S,2R)-3-(((1S)-2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2-HYDROXY-1-( PHENYLMETHYL)PROPYL)-3-((METHYLSULFONYL)(PHENYL)AMINO) BENZAMIDE C33 H42 N4 O5 S PSSKPAZTPVDDNS-RJSONGRPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XFI	PDBBind:  2XFI	IC50: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.198 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.334	α = 90
b = 76.953	β = 90
c = 104.695	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Clarke, B., Cutler, L., Demont, E., Dingwall, C., Dunsdon, R., Hawkins, J., Howes, C., Hussain, I., Maile, G., Matico, R., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Rowland, P., Soleil, V., Smith, K.J., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Wayne, G.

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary