3SKG

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

• PDB DOI: https://doi.org/10.2210/pdb3SKG/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-22 Released: 2011-09-07 
• Deposition Author(s): Muckelbauer, J.K.

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Experimental Data Snapshot

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

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

• PubMed: 21974952 
• 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.

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Organizational Affiliation: 

Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C [auth D], D [auth E]	455	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB8	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-[(3R)-1,2,3,4-tetrahydroisoquinolin-3-yl]propan-2-yl}-4-phenylbutanamide C38 H46 F2 N4 O4 JJJDOYFRIVNWHV-WUCUQKTKSA-N

Binding Affinity Annotations
ID	Source	Binding 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

• Method: X-RAY DIFFRACTION
• 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 = 86.24	α = 90
b = 130.451	β = 96.65
c = 86.872	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Muckelbauer, J.K.

Revision History  

• 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