3R2F | pdb_00003r2f

Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with BMS-693391 AKA (2S)-2-((3R)-3-acetamido-3-isobutyl-2-oxo-1-pyrrolidinyl)-N-((1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-2-((2R,4R)-4-propoxy-2-pyrrolidinyl)ethyl)-4-phenylbutanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 
    0.330 (Depositor), 0.326 (DCC) 
  • R-Value Work: 
    0.280 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 
    0.283 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PB0Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Monosubstituted {gamma}-lactam and conformationally constrained 1,3-diaminopropan-2-ol transition-state isostere inhibitors of {beta}-secretase (BACE).

Boy, K.M.Guernon, J.M.Shi, J.Toyn, J.H.Meredith, J.E.Barten, D.M.Burton, C.R.Albright, C.F.Marcinkeviciene, J.Good, A.C.Tebben, A.J.Muckelbauer, J.K.Camac, D.M.Lentz, K.A.Bronson, J.J.Olson, R.E.Macor, J.E.Thompson, L.A.

(2011) Bioorg Med Chem Lett 21: 6916-6924

  • DOI: https://doi.org/10.1016/j.bmcl.2011.06.109
  • Primary Citation of Related Structures:  
    3R2F

  • PubMed Abstract: 

    The synthesis, evaluation, and structure-activity relationships of a class of γ-lactam 1,3-diaminopropan-2-ol transition-state isostere inhibitors of BACE are discussed. Two strategies for optimizing lead compound 1a are presented. Reducing the overall size of the inhibitors resulted in the identification of γ-lactam 1i, whereas the introduction of conformational constraint on the prime-side of the inhibitor generated compounds such as the 3-hydroxypyrrolidine inhibitor 28n. The full in vivo profile of 1i in rats and 28n in Tg 2576 mice is presented.


  • Organizational Affiliation

    Department of Neuroscience Discovery Chemistry, Research and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, CT 06492, USA. boyk@bms.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1A,
B,
C [auth D],
D [auth E]
455Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PB0 BindingDB:  3R2F IC50: min: 1.4, max: 2 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free:  0.330 (Depositor), 0.326 (DCC) 
  • R-Value Work:  0.280 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 0.283 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.306α = 90
b = 130.255β = 96.53
c = 86.927γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PB0Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary