4ZPF

BACE1 in complex with 8-(3-((1-aminopropan-2-yl)oxy)benzyl)-4-(cyclohexylamino)-1-(3-fluorophenyl)-1,3,8-triazaspiro[4.5]dec-3-en-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Methyl-substitution of an iminohydantoin spiropiperidine beta-secretase (BACE-1) inhibitor has a profound effect on its potency.

Egbertson, M.McGaughey, G.B.Pitzenberger, S.M.Stauffer, S.R.Coburn, C.A.Stachel, S.J.Yang, W.Barrow, J.C.Neilson, L.A.McWherter, M.Perlow, D.Fahr, B.Munshi, S.Allison, T.J.Holloway, K.Selnick, H.G.Yang, Z.Swestock, J.Simon, A.J.Sankaranarayanan, S.Colussi, D.Tugusheva, K.Lai, M.T.Pietrak, B.Haugabook, S.Jin, L.Chen, I.W.Holahan, M.Stranieri-Michener, M.Cook, J.J.Vacca, J.Graham, S.L.

(2015) Bioorg.Med.Chem.Lett. 25: 4812-4819

  • DOI: 10.1016/j.bmcl.2015.06.082
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The IC50 of a beta-secretase (BACE-1) lead compound was improved ∼200-fold from 11 μM to 55 nM through the addition of a single methyl group. Computational chemistry, small molecule NMR, and protein crystallography capabilities were used to compare t ...

    The IC50 of a beta-secretase (BACE-1) lead compound was improved ∼200-fold from 11 μM to 55 nM through the addition of a single methyl group. Computational chemistry, small molecule NMR, and protein crystallography capabilities were used to compare the solution conformation of the ligand under varying pH conditions to its conformation when bound in the active site. Chemical modification then explored available binding pockets adjacent to the ligand. A strategically placed methyl group not only maintained the required pKa of the piperidine nitrogen and filled a small hydrophobic pocket, but more importantly, stabilized the conformation best suited for optimized binding to the receptor.


    Organizational Affiliation

    Medicinal Chemistry Department, WP14-2 Merck and Co., West Point, PA 19486, USA. Electronic address: melissaegbertson@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
405Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4QD
Query on 4QD

Download SDF File 
Download CCD File 
A
8-(3-{[(2S)-1-aminopropan-2-yl]oxy}benzyl)-4-(cyclohexylamino)-1-(3-fluorophenyl)-1,3,8-triazaspiro[4.5]dec-3-en-2-one
C29 H38 F N5 O2
GJCCGBZILLQLCV-NRFANRHFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.720α = 90.00
b = 127.403β = 90.00
c = 77.024γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-05-07 
  • Released Date: 2015-08-05 
  • Deposition Author(s): Orth, P.

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references