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

Experimental Data Snapshot

  • Resolution: 2.88 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.259 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Synthesis and in vivo evaluation of cyclic diaminopropane BACE-1 inhibitors.

Thompson, L.A.Shi, J.Decicco, C.P.Tebben, A.J.Olson, R.E.Boy, K.M.Guernon, J.M.Good, A.C.Liauw, A.Zheng, C.Copeland, R.A.Combs, A.P.Trainor, G.L.Camac, D.M.Muckelbauer, J.K.Lentz, K.A.Grace, J.E.Burton, C.R.Toyn, J.H.Barten, D.M.Marcinkeviciene, J.Meredith, J.E.Albright, C.F.Macor, J.E.

(2011) Bioorg Med Chem Lett 21: 6909-6915

  • DOI: https://doi.org/10.1016/j.bmcl.2011.06.116
  • Primary Citation of Related Structures:  
    3SKF, 3SKG

  • PubMed Abstract: 

    The synthesis, evaluation, and structure-activity relationships of a set of related constrained diaminopropane inhibitors of BACE-1 are described. The full in vivo profile of an optimized inhibitor in both normal and P-gp deficient mice is compared with data generated in normal rats.

  • Organizational Affiliation

    Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA. lorin.thompson@bms.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1A,
C [auth D],
D [auth E]
455Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PB8

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth D],
H [auth E]
C38 H46 F2 N4 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
PB8 PDBBind:  3SKG IC50: 8 (nM) from 1 assay(s)
BindingDB:  3SKG IC50: min: 8.6, max: 9.5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.88 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.259 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.24α = 90
b = 130.451β = 96.65
c = 86.872γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Database references
  • Version 1.2: 2011-11-02
    Changes: Database references
  • Version 1.3: 2012-12-05
    Changes: Database references