Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.14 kDa 
• Atom Count: 3,371 
• Modelled Residue Count: 390 
• Deposited Residue Count: 406 
• Unique protein chains: 1

 4I0Z

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

• PDB DOI:  https://doi.org/10.2210/pdb4I0Z/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: 1.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

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]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-{(1S)-1-[(6-CHLORO-3,3-DIMETHYL-3,4-DIHYDROISOQUINOLIN-1-YL)AMINO]-2-PHENYLETHYL}-4-OXO-1,4-DIHYDROPYRIMIDINE-5-CARBONITRILE	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1BB	B [auth A]	2-{(1S)-1-[(6-chloro-3,3-dimethyl-3,4-dihydroisoquinolin-1-yl)amino]-2-phenylethyl}-4-oxo-1,4-dihydropyrimidine-5-carbonitrile C24 H22 Cl N5 O SSQLUPVACAMCTQ-FQEVSTJZSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1BB	PDBBind:  4I0Z	IC50: 470 (nM) from 1 assay(s)
	Binding MOAD:  4I0Z	IC50: 470 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.168	α = 90
b = 103.852	β = 90
c = 99.765	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
REFMAC	refinement
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