2OF0

X-ray crystal structure of beta secretase complexed with compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1021/jm0611962
  • Structures With Same Primary Citation

  • 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 cata ...

    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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
402Homo sapiensMutation(s): 2 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMZ
Query on CMZ

Download CCD File 
A
(2S)-1-(2,5-dimethylphenoxy)-3-morpholin-4-ylpropan-2-ol
C15 H23 N O3
HVMGGHDPXHODHE-AWEZNQCLSA-N
 Ligand Interaction
IOD
Query on IOD

Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CMZIC50:  1000000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.412α = 90
b = 102.412β = 90
c = 169.237γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling
C-SEARCHphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-01-02 
  • Released Date: 2007-03-13 
  • Deposition Author(s): Patel, S.

Revision History 

  • 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