4I10

Structure-based design of novel dihydroisoquinoline BACE-1 inhibitors that do not engage the catalytic aspartates

• PDB DOI: https://doi.org/10.2210/pdb4I10/pdb

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


• Deposited: 2012-11-19 Released: 2013-03-06 
• Deposition Author(s): Lougheed, J.C., Brecht, E., Yao, N.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.228 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

Literature

Structure-based design of novel dihydroisoquinoline BACE-1 inhibitors that do not engage the catalytic aspartates.

Bowers, S., Xu, Y.Z., Yuan, S., Probst, G.D., Hom, R.K., Chan, W., Konradi, A.W., Sham, H.L., Zhu, Y.L., Beroza, P., Pan, H., Brecht, E., Yao, N., Lougheed, J., Tam, D., Ren, Z., Ruslim, L., Bova, M.P., Artis, D.R.

(2013) Bioorg Med Chem Lett 23: 2181-2186

• PubMed: 23465612 
• DOI: https://doi.org/10.1016/j.bmcl.2013.01.103
• Primary Citation of Related Structures:  
  4HZT, 4I0G, 4I0Z, 4I10, 4I11


• PubMed Abstract: 
  

  The structure-activity relationship of a series of dihydroisoquinoline BACE-1 inhibitors is described. Application of structure-based design to screening hit 1 yielded sub-micromolar inhibitors. Replacement of the carboxylic acid of 1 was guided by X-ray crystallography, which allowed the replacement of a key water-mediated hydrogen bond. This work culminated in compounds such as 31, which possess good BACE-1 potency, excellent permeability and a low P-gp efflux ratio.

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Organizational Affiliation: 

Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 46.1 kDa 
• Atom Count: 3,362 
• Modelled Residue Count: 390 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1BS	E [auth A]	2-{(1S)-1-[(6-chloro-3,3-dimethyl-3,4-dihydroisoquinolin-1-yl)amino]-2-phenylethyl}pyrido[4,3-d]pyrimidin-4(1H)-one C26 H24 Cl N5 O DQYKHJYAOKSEPD-QFIPXVFZSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1BS	PDBBind:  4I10	IC50: 170 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.228 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.09	α = 90
b = 103.9	β = 90
c = 99.72	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Lougheed, J.C., Brecht, E., Yao, N.H.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2013-04-24
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary