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


Ligand Structure Quality Assessment 


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: https://doi.org/10.1016/j.bmcl.2014.10.006
  • Primary Citation of Related Structures:  
    4R8Y, 4R91, 4R92, 4R93, 4R95

  • 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 with sub-micromolar potency ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
414Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
779
Query on 779
Download Ideal Coordinates CCD File 
E [auth A],
G [auth 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 Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B]		L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
779 BindingDB:  4R93 Ki: 16 (nM) from 1 assay(s)
Binding MOAD:  4R93 Ki: 16 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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