3SKF

Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with (2S)-2-((3S)-3-(acetylamino)-3-(butan-2-yl)-2-oxopyrrolidin-1-yl)-N-((2S,3R)-3-hydroxy-4-((3-methoxybenzyl)amino)-1-phenylbutan-2-yl)-4-phenylbutanamide

• PDB DOI: https://doi.org/10.2210/pdb3SKF/pdb

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


• Deposited: 2011-06-22 Released: 2011-08-31 
• Deposition Author(s): Muckelbauer, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.313 
• R-Value Work: 0.252 
• R-Value Observed: 0.256 

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)

Macromolecule Content

• Total Structure Weight: 101.98 kDa 
• Atom Count: 6,361 
• Modelled Residue Count: 774 
• Deposited Residue Count: 910 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB7	C [auth A], E [auth B]	(2S)-2-{(3S)-3-(acetylamino)-3-[(2S)-butan-2-yl]-2-oxopyrrolidin-1-yl}-N-{(2S,3R)-3-hydroxy-4-[(3-methoxybenzyl)amino]-1-phenylbutan-2-yl}-4-phenylbutanamide C38 H50 N4 O5 SMPAHDBHYSCFQF-SXXDCNOLSA-N
IOD	D [auth A], F [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
PB7	PDBBind:  3SKF	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.313 
• R-Value Work: 0.252 
• R-Value Observed: 0.256 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.288	α = 90
b = 130.264	β = 90
c = 85.871	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
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references
• Version 1.2: 2011-11-02
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary