3HW1

Structure of Bace (beta secretase) in complex with ligand EV2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-Based Discovery of BACE1 Inhibitors Using Functional Assays

Godemann, R.Madden, J.Kramer, J.Smith, M.A.Fritz, U.Hesterkamp, T.Barker, J.Hoeppner, S.Hallett, D.Cesura, A.Ebneth, A.Kemp, J.

(2009) Biochemistry 48: 10743-10751

  • DOI: 10.1021/bi901061a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Novel nonpeptidic inhibitors of beta-secretase (BACE1) have been discovered by employing a fragment-based biochemical screening approach. A diverse library of 20000 low-molecular weight compounds were screened and yielded 26 novel hits that were conf ...

    Novel nonpeptidic inhibitors of beta-secretase (BACE1) have been discovered by employing a fragment-based biochemical screening approach. A diverse library of 20000 low-molecular weight compounds were screened and yielded 26 novel hits that were confirmed by biochemical and surface plasmon resonance secondary assays. We describe here fragment inhibitors cocrystallized with BACE1 in a flap open and flap closed conformation as determined by X-ray crystallography.


    Organizational Affiliation

    Evotec AG, Schnackenburgallee 114, 22525 Hamburg, Germany. robert.godemann@evotec.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B, C
411Homo sapiensMutation(s): 2 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EV2
Query on EV2

Download SDF File 
Download CCD File 
A, B, C
3-pyrrolidin-1-ylquinoxalin-2-amine
C12 H14 N4
LWWDIFFPFOZSSB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EV2IC50: 870000 nM BINDINGMOAD
EV2IC50: 870000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 230.625α = 90.00
b = 99.880β = 103.12
c = 62.900γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SLSPXdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance