Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.25 kDa 
• Atom Count: 3307 
• Residue Count: 375 
• Unique protein chains: 1

4DPF

BACE-1 in complex with a HEA-macrocyclic type inhibitor

• DOI: 10.2210/pdb4DPF/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-13 Released: 2012-07-11 
• Deposition Author(s): Lindberg, J., Borkakoti, N., Derbyshire, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Highly potent macrocyclic BACE-1 inhibitors incorporating a hydroxyethylamine core: design, synthesis and X-ray crystal structures of enzyme inhibitor complexes.

Sandgren, V., Agback, T., Johansson, P.O., Lindberg, J., Kvarnstrom, I., Samuelsson, B., Belda, O., Dahlgren, A.

(2012) Bioorg Med Chem 20: 4377-4389

• PubMed: 22698785 
• DOI: 10.1016/j.bmc.2012.05.039
• Primary Citation of Related Structures:  
  4DPI, 4DPF


• PubMed Abstract: 
  

A series of P1-P3 linked macrocyclic BACE-1 inhibitors containing a hydroxyethylamine (HEA) isostere scaffold has been synthesized. All inhibitors comprise a toluene or N-phenylmethanesulfonamide P2 moiety. Excellent BACE-1 potencies, both in enzymatic and cell-based assays, were observed in this series of target compounds, with the best candidates displaying cell-based IC(50) values in the low nanomolar range. As an attempt to improve potency, a phenyl substituent aiming at the S3 subpocket was introduced in the macrocyclic ring. X-ray analyzes were performed on selected compounds, and enzyme-inhibitor interactions are discussed.

---

Organizational Affiliation: 

Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	391	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817 GTEx  ENSG00000186318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0LG	A	N-[(4S,8E,11S)-4-[(1R)-1-hydroxy-2-{[3-(propan-2-yl)benzyl]amino}ethyl]-2,13-dioxo-11-phenyl-6-oxa-3,12-diazabicyclo[12.3.1]octadeca-1(18),8,14,16-tetraen-16-yl]-N-methylmethanesulfonamide C35 H44 N4 O6 S XYJDOUBLYLOJJL-YNYOQIOBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0LG	IC50:  400   nM  BindingDB
0LG	IC50:  260   nM  BindingDB
0LG	IC50:  400   nM  Binding MOAD
0LG	IC50 :  400   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.76	α = 90
b = 76.71	β = 90
c = 103.88	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-13 
• Released Date: 2012-07-11 
Deposition Author(s): Lindberg, J., Borkakoti, N., Derbyshire, D.

Revision History 

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references