3L5E

Structure of BACE Bound to SCH736062


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of Cyclic Acylguanidines as Highly Potent and Selective beta-Site Amyloid Cleaving Enzyme (BACE) Inhibitors: Part I-Inhibitor Design and Validation

Zhu, Z.Sun, Z.Y.Ye, Y.Voigt, J.Strickland, C.Smith, E.M.Cumming, J.Wang, L.Wong, J.Wang, Y.S.Wyss, D.F.Chen, X.Kuvelkar, R.Kennedy, M.E.Favreau, L.Parker, E.McKittrick, B.A.Stamford, A.Czarniecki, M.Greenlee, W.Hunter, J.C.

(2010) J.Med.Chem. 53: 951-965

  • DOI: 10.1021/jm901408p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A number of novel amidine containing heterocycles were designed to reproduce the unique interaction pattern, revealed by X-ray crystallography, between the BACE-1 catalytic diad and a weak NMR screening hit (3), with special attention paid to maintai ...

    A number of novel amidine containing heterocycles were designed to reproduce the unique interaction pattern, revealed by X-ray crystallography, between the BACE-1 catalytic diad and a weak NMR screening hit (3), with special attention paid to maintaining the appropriate basicity and limiting the number of H-bonding donors of these scaffolds. The iminohydantoin cores (10 and 23) were examined first and found to interact with the catalytic diad in one of two binding modes (A and B), each with the iminohydantoin core flipped 180 degrees in relation to the other. The amidine structural motif within each core forms a bidentate interaction with a different aspartic acid of the catalytic diad. Both modes reproduced a highly conserved interaction pattern between the inhibitors and the catalytic aspartates, as revealed by 3. Potent iminohydantoin BACE-1 inhibitors have been obtained, validating the molecular design as aspartyl protease catalytic site inhibitors. Brain penetrant small molecule BACE inhibitors with high ligand efficiencies have been discovered, enabling multiple strategies for further development of these inhibitors into highly potent, selective and in vivo efficacious BACE inhibitors.


    Organizational Affiliation

    Department of Medicinal Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA. Zhaoning.Zhu@spcorp.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B
414Homo sapiensMutation(s): 0 
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
BDW
Query on BDW

Download SDF File 
Download CCD File 
A, B
(4S)-1-(4-{[(2Z,4R)-4-(2-cyclohexylethyl)-4-(cyclohexylmethyl)-2-imino-5-oxoimidazolidin-1-yl]methyl}benzyl)-4-propylimidazolidin-2-one
C32 H49 N5 O2
SILGEXOUELDSRZ-GMCHKSTQSA-N
 Ligand Interaction
TAR
Query on TAR

Download SDF File 
Download CCD File 
A, B
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BDWKi: 27 nM (100) BINDINGDB
BDWIC50: 27 nM BINDINGMOAD
BDWIC50: 27 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.478α = 90.00
b = 89.469β = 90.00
c = 130.645γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CNSphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description