4DJW

Structure of BACE Bound to 2-imino-3-methyl-5-phenyl-5-(3-(pyridin-3-yl)phenyl)imidazolidin-4-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor.

Cumming, J.N.Smith, E.M.Wang, L.Misiaszek, J.Durkin, J.Pan, J.Iserloh, U.Wu, Y.Zhu, Z.Strickland, C.Voigt, J.Chen, X.Kennedy, M.E.Kuvelkar, R.Hyde, L.A.Cox, K.Favreau, L.Czarniecki, M.F.Greenlee, W.J.McKittrick, B.A.Parker, E.M.Stamford, A.W.

(2012) Bioorg.Med.Chem.Lett. 22: 2444-2449

  • DOI: 10.1016/j.bmcl.2012.02.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • From an initial lead 1, a structure-based design approach led to identification of a novel, high-affinity iminohydantoin BACE1 inhibitor that lowers CNS-derived Aβ following oral administration to rats. Herein we report SAR development in the S3 and ...

    From an initial lead 1, a structure-based design approach led to identification of a novel, high-affinity iminohydantoin BACE1 inhibitor that lowers CNS-derived Aβ following oral administration to rats. Herein we report SAR development in the S3 and F' subsites of BACE1 for this series, the synthetic approaches employed in this effort, and in vivo data for the optimized compound.


    Organizational Affiliation

    Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA. jared.cumming@merck.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
TLA
Query on TLA

Download SDF File 
Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
0KP
Query on 0KP

Download SDF File 
Download CCD File 
A, B
(2E,5R)-2-imino-3-methyl-5-phenyl-5-[3-(pyridin-3-yl)phenyl]imidazolidin-4-one
C21 H18 N4 O
PNSQCPQDRVOKMA-OAQYLSRUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0KPKi: 110 nM (100) BINDINGDB
0KPIC50: 630 nM (100) BINDINGDB
0KPKi: 530 nM BINDINGMOAD
0KPKi: 530 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.550α = 90.00
b = 89.639β = 90.00
c = 131.013γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement
CrystalCleardata collection
CNSphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Database references