Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 44.30 kDa 
• Atom Count: 3368 
• Residue Count: 374 
• Unique protein chains: 1

2VIE

Human BACE-1 in complex with N-((1S,2R)-1-benzyl-2-hydroxy-3-((1,1,5- trimethylhexyl)amino)propyl)-3-(ethylamino)-5-(2-oxopyrrolidin-1-yl) benzamide

• DOI: 10.2210/pdb2VIE/pdb

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


• Deposited: 2007-11-30 Released: 2008-01-29 
• Deposition Author(s): Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Faller, A., Hawkins, J., Hussain, I., MacPherson, D., Maile, G., Matico, R., Milner, P., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Riddell, D., Rowland, P., Soleil, V., Smith, K., Stanway, S., Stemp, G., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Ward, J., Wayne, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.191 

Literature

Bace-1 Inhibitors Part 2: Identification of Hydroxy Ethylamines (Heas) with Reduced Peptidic Character.

Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Faller, A., Hawkins, J., Hussain, I., Macpherson, D., Maile, G., Matico, R., Milner, P., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Riddell, D., Rowland, P., Soleil, V., Smith, K., Stanway, S., Stemp, G., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Ward, J., Wayne, G.

(2008) Bioorg Med Chem Lett 18: 1017

• PubMed: 18166458 
• DOI: 10.1016/j.bmcl.2007.12.019
• Primary Citation of Related Structures:  
  2VJ6, 2VJ7, 2VJ9, 2VIE


• PubMed Abstract: 
  

This paper describes the discovery of non-peptidic, potent, and selective hydroxy ethylamine (HEA) inhibitors of BACE-1 by replacement of the prime side of a lead di-amide 2. Inhibitors with nanosmolar potency and high selectivity were identified. Depending on the nature of the P(1)(') and P(2)(') substituents, two different binding modes were observed in X-ray co-crystal structures.

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Organizational Affiliation: 

Neurology and Gastrointestinal Centre of Excellence for Drug Discovery, GlaxoSmithKline R&D, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	392	Homo sapiens	Mutation(s): 4  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
VG0	A	N-{(1S,2R)-1-benzyl-2-hydroxy-3-[(1,1,5-trimethylhexyl)amino]propyl}-3-(ethylamino)-5-(2-oxopyrrolidin-1-yl)benzamide C32 H48 N4 O3 BNTVCVCCNARYIP-URLMMPGGSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
VG0	IC50:  230   nM  BindingDB
VG0	IC50:  210   nM  BindingDB
VG0	IC50 :  33   nM  PDBBind
VG0	IC50:  33   nM  Binding MOAD
VG0	IC50:  33   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.921	α = 90
b = 75.848	β = 90
c = 104.532	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-30 
• Released Date: 2008-01-29 
Deposition Author(s): Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Faller, A., Hawkins, J., Hussain, I., MacPherson, D., Maile, G., Matico, R., Milner, P., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Riddell, D., Rowland, P., Soleil, V., Smith, K., Stanway, S., Stemp, G., Sweitzer, S., Theobald, P., Vesey, D., Walter, D.S., Ward, J., Wayne, G.

Revision History 

• Version 1.0: 2008-01-29
  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