4R93

BACE-1 in complex with (R)-4-(2-cyclohexylethyl)-1-methyl-5-oxo-4-(((1S,3R)-3-(3-phenylureido)cyclohexyl)methyl)imidazolidin-2-iminium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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:  
    4R93, 4R95, 4R8Y, 4R91, 4R92

  • 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1AB414Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
779
Query on 779

Download CCD File 
A, B
1-[(1R,3S)-3-{[(2E,4R)-4-(2-cyclohexylethyl)-2-imino-1-methyl-5-oxoimidazolidin-4-yl]methyl}cyclohexyl]-3-phenylurea
C26 H39 N5 O2
CVMRAJSOLFSMNH-UNIVCBNLSA-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 %)
779Ki:  16   nM  BindingDB
779Ki:  16   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.49α = 90
b = 89.33β = 90
c = 130.95γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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