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: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 F' subsites of BACE1 for this series, the synthetic approaches employed in this effort, and in vivo data for the optimized compound ...

    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 1A, B414Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0KP (Subject of Investigation/LOI)
Query on 0KP

Download Ideal Coordinates CCD File 
C [auth A], E [auth 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
TLA
Query on TLA

Download Ideal Coordinates CCD File 
D [auth A], F [auth B], G [auth B]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0KP Binding MOAD:  4DJW Ki: 530 (nM) from 1 assay(s)
PDBBind:  4DJW Ki: 530 (nM) from 1 assay(s)
BindingDB:  4DJW Ki: 110 (nM) from 1 assay(s)
IC50: min: 630, max: 1680 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.55α = 90
b = 89.639β = 90
c = 131.013γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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