3R2F

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 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.283 

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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: 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 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
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A,
B,
C [auth D],
D [auth E]		455Homo sapiensMutation(s): 0 
Gene Names: BACE, BACE1, 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PB0
Query on PB0
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth D],
H [auth E]		(2S)-2-[(3R)-3-(acetylamino)-3-(2-methylpropyl)-2-oxopyrrolidin-1-yl]-N-{(1R,2S)-3-(3,5-difluorophenyl)-1-hydroxy-1-[(2R,4R)-4-propoxypyrrolidin-2-yl]propan-2-yl}-4-phenylbutanamide
C36 H50 F2 N4 O5
LPZOLMFQGUDKQH-ZXWXCOCLSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PB0 BindingDB:  3R2F IC50: min: 1.4, max: 2 (nM) from 2 assay(s)
PDBBind:  3R2F IC50: 1.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.283 
  • 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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2011-03-14 
  • Released Date: 2011-08-31 
    • Deposition Author(s): Muckelbauer, J.K.

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