3HVG

Structure of bace (beta secretase) in Complex with EV0

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    3HVG, 3HW1

  • 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 confirmed by biochemical and surface plasmon resonance secondary assays ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C411Homo sapiensMutation(s): 2 
Gene Names: BACE1, BACE, KIAA1149
EC: 3.4.23.46
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EV0
Query on EV0
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth B]		2-amino-6-propylpyrimidin-4(3H)-one
C7 H11 N3 O
FSYKBAWAYYELHH-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EV0 BindingDB:  3HVG Kd: 4.45e+6 (nM) from 1 assay(s)
IC50: 2.49e+6 (nM) from 1 assay(s)
Binding MOAD:  3HVG IC50: 2.00e+6 (nM) from 1 assay(s)
PDBBind:  3HVG IC50: 2.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 232.55α = 90
b = 100.13β = 103.73
c = 64.78γ = 90
Software Package:
Software NamePurpose
SLSPXdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2018-01-31
    Changes: Experimental preparation
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations