3EXO

Crystal structure of BACE1 bound to inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of a small molecule beta-secretase inhibitor that binds without catalytic aspartate engagement.

Steele, T.G.Hills, I.D.Nomland, A.A.de Leon, P.Allison, T.McGaughey, G.Colussi, D.Tugusheva, K.Haugabook, S.J.Espeseth, A.S.Zuck, P.Graham, S.L.Stachel, S.J.

(2009) Bioorg.Med.Chem.Lett. 19: 17-20

  • DOI: 10.1016/j.bmcl.2008.11.027

  • PubMed Abstract: 
  • A small molecule inhibitor of beta-secretase with a unique binding mode has been developed. Crystallographic determination of the enzyme-inhibitor complex shows the catalytic aspartate residues in the active site are not engaged in inhibitor binding. ...

    A small molecule inhibitor of beta-secretase with a unique binding mode has been developed. Crystallographic determination of the enzyme-inhibitor complex shows the catalytic aspartate residues in the active site are not engaged in inhibitor binding. This unprecedented binding mode in the field of aspartyl protease inhibition is described.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co, West Point, PA 19486, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
413Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5MS
Query on 5MS

Download SDF File 
Download CCD File 
A
N-{2-methyl-5-[(6-phenylpyrimidin-4-yl)amino]phenyl}methanesulfonamide
C18 H18 N4 O2 S
CXQRKICWSCAUGW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5MSIC50: 24000 nM (99) BINDINGDB
5MSIC50: 24000 nM BINDINGMOAD
5MSIC50: 24000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 104.433α = 90.00
b = 127.923β = 90.00
c = 76.671γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
StructureStudiodata collection
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-10-16 
  • Released Date: 2009-02-03 
  • Deposition Author(s): Allison, T.J.

Revision History 

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description