4DJV

Structure of BACE Bound to 2-imino-5-(3'-methoxy-[1,1'-biphenyl]-3-yl)-3-methyl-5-phenylimidazolidin-4-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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:  
    4DJU, 4DJV, 4DJW, 4DJX, 4DJY

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1AB414Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0KM
Query on 0KM

Download CCD File 
A, B
(2E,5R)-2-imino-5-(3'-methoxybiphenyl-3-yl)-3-methyl-5-phenylimidazolidin-4-one
C23 H21 N3 O2
LRYKHTDVFXMHEH-HSZRJFAPSA-N
 Ligand Interaction
TLA
Query on TLA

Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0KMKi:  190   nM  Binding MOAD
0KMKi :  190   nM  PDBBind
0KMIC50:  392   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.503α = 90
b = 89.743β = 90
c = 131.04γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
CNSphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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