3IVH

Design and Synthesis of Potent BACE-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents

• PDB DOI: https://doi.org/10.2210/pdb3IVH/pdb

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


• Deposited: 2009-09-01 Released: 2010-01-05 
• Deposition Author(s): Pan, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Design and synthesis of cell potent BACE-1 inhibitors: structure-activity relationship of P1' substituents.

Sealy, J.M., Truong, A.P., Tso, L., Probst, G.D., Aquino, J., Hom, R.K., Jagodzinska, B.M., Dressen, D., Wone, D.W., Brogley, L., John, V., Tung, J.S., Pleiss, M.A., Tucker, J.A., Konradi, A.W., Dappen, M.S., Toth, G., Pan, H., Ruslim, L., Miller, J., Bova, M.P., Sinha, S., Quinn, K.P., Sauer, J.M.

(2009) Bioorg Med Chem Lett 19: 6386-6391

• PubMed: 19811916 
• DOI: https://doi.org/10.1016/j.bmcl.2009.09.061
• Primary Citation of Related Structures:  
  3IVH, 3IVI


• PubMed Abstract: 
  

  Using structure-guided design, hydroxyethylamine BACE-1 inhibitors were optimized to nanomolar Abeta cellular inhibition with selectivity against cathepsin-D. X-ray crystallography illuminated the S1' residues critical to this effort, which culminated in compounds 56 and 57 that exhibited potency and selectivity but poor permeability and high P-gp efflux.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Elan Pharmaceuticals, 180 Oyster Point Boulevard, 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)

Macromolecule Content

• Total Structure Weight: 45.92 kDa 
• Atom Count: 3,263 
• Modelled Residue Count: 379 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	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
1LI	B [auth A]	N-[(1S,2R)-3-{[1-(3-tert-butylphenyl)cyclohexyl]amino}-1-(3,5-difluorobenzyl)-2-hydroxypropyl]acetamide C28 H38 F2 N2 O2 RJXIEHBFRZLGTH-IZZNHLLZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1LI	PDBBind:  3IVH	IC50: 47 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.924	α = 90
b = 105.181	β = 95.25
c = 51.029	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-05 
Deposition Author(s): Pan, H.

Revision History  

• Version 1.0: 2010-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary