3NSH

BACE-1 in complex with ELN475957

• PDB DOI: https://doi.org/10.2210/pdb3NSH/pdb

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


• Deposited: 2010-07-01 Released: 2010-09-22 
• Deposition Author(s): Probst, G.D., Bowers, S., Sealy, J.M., Brecht, E., Yao, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.279 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 

Literature

Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors: structure-activity relationship of the aryl region.

Probst, G.D., Bowers, S., Sealy, J.M., Stupi, B., Dressen, D., Jagodzinska, B.M., Aquino, J., Gailunas, A., Truong, A.P., Tso, L., Xu, Y.Z., Hom, R.K., John, V., Tung, J.S., Pleiss, M.A., Tucker, J.A., Konradi, A.W., Sham, H.L., Jagodzinski, J., Toth, G., Brecht, E., Yao, N., Pan, H., Lin, M., Artis, D.R., Ruslim, L., Bova, M.P., Sinha, S., Yednock, T.A., Gauby, S., Zmolek, W., Quinn, K.P., Sauer, J.M.

(2010) Bioorg Med Chem Lett 20: 6034-6039

• PubMed: 20822903 
• DOI: https://doi.org/10.1016/j.bmcl.2010.08.070
• Primary Citation of Related Structures:  
  3NSH


• PubMed Abstract: 
  

  The structure-activity relationship of the prime region of hydroxyethylamine BACE inhibitors is described. Variation in the aryl linker region with 5- and 6-membered heterocycles provided compounds such as 33 with improved permeability and reduced P-gp liability compared to benzyl amine analog 1.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Elan Pharmaceuticals, South San Francisco, CA 94080, USA.

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)

Macromolecule Content

• Total Structure Weight: 137.69 kDa 
• Atom Count: 9,293 
• Modelled Residue Count: 1,124 
• Deposited Residue Count: 1,218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	406	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
957	D [auth A], E [auth B], F [auth C]	N-[(1S,2R)-1-(3,5-difluorobenzyl)-3-({1-[4-(2,2-dimethylpropyl)thiophen-2-yl]cyclopropyl}amino)-2-hydroxypropyl]acetamide C24 H32 F2 N2 O2 S YEGCCSKZPHGALE-LEWJYISDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
957	PDBBind:  3NSH	IC50: 470 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.279 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.155	α = 90
b = 104.592	β = 104.5
c = 100.155	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Probst, G.D., Bowers, S., Sealy, J.M., Brecht, E., Yao, N.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations