X-ray crystal structure of beta secretase complexed with 2-aminoquinoline

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

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This is version 1.5 of the entry. See complete history


Application of fragment screening by X-ray crystallography to beta-Secretase.

Murray, C.W.Callaghan, O.Chessari, G.Cleasby, A.Congreve, M.Frederickson, M.Hartshorn, M.J.McMenamin, R.Patel, S.Wallis, N.

(2007) J Med Chem 50: 1116-1123

  • DOI: https://doi.org/10.1021/jm0611962
  • Primary Citation of Related Structures:  
    2OF0, 2OHK, 2OHL, 2OHM, 2OHN

  • PubMed Abstract: 

    This paper describes an application of fragment screening to the aspartyl protease enzyme, beta-secretase (BACE-1), using high throughput X-ray crystallography. Three distinct chemotypes were identified by X-ray crystallography as binding to the catalytic aspartates either via an aminoheterocycle (such as 2-aminoquinoline), a piperidine, or an aliphatic hydroxyl group. The fragment hits were weak inhibitors of BACE-1 in the millimolar range but were of interest because most of them displayed relatively good ligand efficiencies. The aminoheterocycles exhibited a novel recognition motif that has not been seen before with aspartic proteases. Virtual screening around this motif identified an aminopyridine with increased potency and attractive growth points for further elaboration using structure-based drug design. The companion paper illustrates how sub-micromolar inhibitors were developed starting from this fragment.

  • Organizational Affiliation

    Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom. c.murray@astex-therapeutics.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1402Homo sapiensMutation(s): 2 
Gene Names: BACE1BACE
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
2AQ PDBBind:  2OHL Kd: 9.00e+5 (nM) from 1 assay(s)
BindingDB:  2OHL Kd: 9.00e+5 (nM) from 1 assay(s)
IC50: min: 8.00e+5, max: 2.00e+6 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.833α = 90
b = 102.833β = 90
c = 168.85γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2007-03-13 
  • Deposition Author(s): Patel, S.

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2021-10-20
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description