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

• PDB DOI:  https://doi.org/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: https://doi.org/10.1016/j.bmcl.2007.12.019
• Primary Citation of Related Structures:  
  2VIE, 2VJ6, 2VJ7, 2VJ9


• 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.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 44.3 kDa 
• Atom Count: 3,368 
• Modelled Residue Count: 374 
• 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  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VG0	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
VG0	BindingDB:  2VIE	IC50: min: 33, max: 230 (nM) from 3 assay(s)
	PDBBind:  2VIE	IC50: 33 (nM) from 1 assay(s)
	Binding MOAD:  2VIE	IC50: 33 (nM) from 1 assay(s)

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

• 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