4R91

BACE-1 in complex with (R)-4-(2-cyclohexylethyl)-4-(((1S,3R)-3-(cyclopentylamino)cyclohexyl)methyl)-1-methyl-5-oxoimidazolidin-2-iminium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of potent iminoheterocycle BACE1 inhibitors.

Caldwell, J.P.Mazzola, R.D.Durkin, J.Chen, J.Chen, X.Favreau, L.Kennedy, M.Kuvelkar, R.Lee, J.McHugh, N.McKittrick, B.Orth, P.Stamford, A.Strickland, C.Voigt, J.Wang, L.Zhang, L.Zhang, Q.Zhu, Z.

(2014) Bioorg.Med.Chem.Lett. 24: 5455-5459

  • DOI: 10.1016/j.bmcl.2014.10.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The synthesis of a series of iminoheterocycles and their structure-activity relationships (SAR) as inhibitors of the aspartyl protease BACE1 will be detailed. An effort to access the S3 subsite directly from the S1 subsite initially yielded compounds ...

    The synthesis of a series of iminoheterocycles and their structure-activity relationships (SAR) as inhibitors of the aspartyl protease BACE1 will be detailed. An effort to access the S3 subsite directly from the S1 subsite initially yielded compounds with sub-micromolar potency. A subset of compounds from this effort unexpectedly occupied a different binding site and displayed excellent BACE1 affinities. Select compounds from this subset acutely lowered Aβ40 levels upon subcutaneous and oral administration to rats.


    Organizational Affiliation

    Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: john.caldwell@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
3KT
Query on 3KT

Download SDF File 
Download CCD File 
A, B
(2E,5R)-5-(2-cyclohexylethyl)-5-{[(1S,3R)-3-(cyclopentylamino)cyclohexyl]methyl}-2-imino-3-methylimidazolidin-4-one
C24 H42 N4 O
NOZCXTAZEGFFAQ-XZDHIHRUSA-N
 Ligand Interaction
TLA
Query on TLA

Download SDF File 
Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3KTKi: 430 nM (100) BINDINGDB
3KTKi: 430 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.410α = 90.00
b = 89.550β = 90.00
c = 131.070γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-12-17
    Type: Database references