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

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.bmc.2012.05.039
  • Primary Citation of Related Structures:  
    4DPF, 4DPI

  • 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1391Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0LG

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
0LG Binding MOAD:  4DPF IC50: 400 (nM) from 1 assay(s)
BindingDB:  4DPF IC50: min: 260, max: 400 (nM) from 2 assay(s)
PDBBind:  4DPF IC50: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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 = 47.76α = 90
b = 76.71β = 90
c = 103.88γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PDB_EXTRACTdata extraction
DNAdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

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