3SKG | pdb_00003skg

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 
    0.348 (Depositor) 
  • R-Value Work: 
    0.255 (Depositor) 
  • R-Value Observed: 
    0.259 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3SKG

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

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 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

Macromolecule Content 

  • Total Structure Weight: 203.53 kDa 
  • Atom Count: 12,434 
  • Modeled Residue Count: 1,544 
  • Deposited Residue Count: 1,820 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-secretase 1A,
B,
C [auth D],
D [auth E]		455Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000186318 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
PB8 BindingDB:  3SKG IC50: min: 8.6, max: 9.5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free:  0.348 (Depositor) 
  • R-Value Work:  0.255 (Depositor) 
  • R-Value Observed: 0.259 (Depositor) 
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
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata 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

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
  • Version 1.4: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary