Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.68 kDa 
• Atom Count: 3022 
• Modelled Residue Count: 373 
• Deposited Residue Count: 433 
• Unique protein chains: 1

4IVS

Crystal structure of BACE1 with its inhibitor

• PDB DOI: 10.2210/pdb4IVS/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-01-23 Released: 2013-11-13 
• Deposition Author(s): Chen, T.T., Li, L., Chen, W.Y., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.227 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Literature

Virtual screening and structure-based discovery of indole acylguanidines as potent beta-secretase (BACE1) inhibitors

Zou, Y., Li, L., Chen, W.Y., Chen, T.T., Ma, L., Wang, X., Xiong, B., Xu, Y.C., Shen, J.

(2013) Molecules 18: 5706-5722

• PubMed: 23681056 
• DOI: 10.3390/molecules18055706
• Primary Citation of Related Structures:  
  4IVS, 4IVT


• PubMed Abstract: 
  

Proteolytic cleavage of amyloid precursor protein by β-secretase (BACE1) is a key step in generating the N-terminal of β-amyloid (Aβ), which further forms into amyloid plaques that are considered as the hallmark of Alzheimer's disease. Inhibitors of BACE1 can reduce the levels of Aβ and thus have a therapeutic potential for treating the disease. We report here the identification of a series of small molecules bearing an indole acylguanidine core structure as potent BACE1 inhibitors. The initial weak fragment was discovered by virtual screening, and followed with a hit-to-lead optimization. With the aid of co-crystal structures of two discovered inhibitors (compounds 19 and 25) with BACE1, we explored the SAR around the indole and aryl groups, and obtained several BACE1 inhibitors about 1,000-fold more potent than the initial fragment hit. Accompanying the lead optimization, a previously under-explored sub-site opposite the flap loop was redefined as a potential binding site for later BACE1 inhibitor design.

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Organizational Affiliation: 

State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	433	Homo sapiens	Mutation(s): 2  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
VSI	B [auth A]	N-{N-[4-(acetylamino)-3,5-dichlorobenzyl]carbamimidoyl}-2-(6-cyano-1H-indol-1-yl)acetamide C21 H18 Cl2 N6 O2 QNSBKNRQYCQXMO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VSI	PDBBind:  4IVS	IC50: 44 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.227 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.883	α = 90
b = 129.376	β = 90
c = 77.249	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-23 
• Released Date: 2013-11-13 
Deposition Author(s): Chen, T.T., Li, L., Chen, W.Y., Xu, Y.C.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release