2VIJ | pdb_00002vij

Human BACE-1 in complex with 3-(1,1-dioxidotetrahydro-2H-1,2-thiazin- 2-yl)-5-(ethylamino)-N-((1S,2R)-2-hydroxy-1-(phenylmethyl)-3-(1,2,3,4- tetrahydro-1-naphthalenylamino)propyl)benzamide

• PDB DOI: https://doi.org/10.2210/pdb2VIJ/pdb

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


• Deposited: 2007-12-04 Released: 2008-01-29 
• Deposition Author(s): Beswick, P., Charrier, N., Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Faller, A., Gleave, R., Hawkins, J., Hussain, I., Johnson, C.N., Macpherson, D., Maile, G., Matico, R., Milner, P., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Riddell, D., Rowland, P., Skidmore, J., Soleil, V., Smith, K.J., Stanway, S., Stemp, G., Stuart, A., 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: 1.60 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.184 (DCC) 

Literature

Bace-1 Inhibitors Part 3: Identification of Hydroxy Ethylamines (Heas) with Nanomolar Potency in Cells.

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

(2008) Bioorg Med Chem Lett 18: 1022

• PubMed: 18171615 
• DOI: https://doi.org/10.1016/j.bmcl.2007.12.020
• Primary Citation Related Structures: 
  2VIJ


• PubMed Abstract: 
  

  This article is focusing on further optimization of previously described hydroxy ethylamine (HEA) BACE-1 inhibitors obtained from a focused library with the support of X-ray crystallography. Optimization of the non-prime side of our inhibitors and introduction of a 6-membered sultam substituent binding to Asn-294 as well as a fluorine in the C-2 position led to derivatives with nanomolar potency in cell-based assays.

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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, UK.

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: 44.94 kDa 
• Atom Count: 3,448 
• Modeled 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  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
C44	B [auth A], C [auth A]	N-{(1S,2R)-1-benzyl-2-hydroxy-3-[(1S)-1,2,3,4-tetrahydronaphthalen-1-ylamino]propyl}-3-(1,1-dioxido-1,2-thiazinan-2-yl)-5-(ethylamino)benzamide C33 H42 N4 O4 S OAOKRIOFVOASEG-OWHBQTKESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.184 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.952	α = 90
b = 76.734	β = 90
c = 105.286	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-29 
Deposition Author(s): Beswick, P., Charrier, N., Clarke, B., Demont, E., Dingwall, C., Dunsdon, R., Faller, A., Gleave, R., Hawkins, J., Hussain, I., Johnson, C.N., Macpherson, D., Maile, G., Matico, R., Milner, P., Mosley, J., Naylor, A., O'Brien, A., Redshaw, S., Riddell, D., Rowland, P., Skidmore, J., Soleil, V., Smith, K.J., Stanway, S., Stemp, G., Stuart, A., 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
• Version 1.5: 2019-09-18
  Changes: Data collection
• Version 1.6: 2024-11-13
  Changes: Data collection, Database references, Other, Structure summary