3FKT

Crystal Structure of Human Beta Secretase Complexed with Spiropiperdine Iminohydantoin Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery and X-ray Crystallographic Analysis of a Iminohydantoin Inhibitor of beta-Secretase

Barrow, J.C.Stauffer, S.R.Rittle, K.E.Ngo, P.L.Yang, M.S.Graham, S.McGaughey, G.Holloway, K.Tugusheva, S.K.Lai, M.Espeseth, A.S.Xu, M.Huang, Q.Zuck, P.Levorse, D.A.Hazuda, D.Vacca, J.P.

(2008) J.Med.Chem. 51: 6259-6262

  • DOI: 10.1021/jm800914n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A high-throughput screen at 100 microM inhibitor concentration for the BACE-1 enzyme revealed a novel spiropiperidine iminohydantoin aspartyl protease inhibitor template. An X-ray cocrystal structure with BACE-1 revealed a novel mode of binding where ...

    A high-throughput screen at 100 microM inhibitor concentration for the BACE-1 enzyme revealed a novel spiropiperidine iminohydantoin aspartyl protease inhibitor template. An X-ray cocrystal structure with BACE-1 revealed a novel mode of binding whereby the inhibitor interacts with the catalytic aspartates via bridging water molecules. Using the crystal structure as a guide, potent compounds with good brain penetration were designed.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA. james_barrow@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
405Homo sapiensMutation(s): 2 
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
SII
Query on SII

Download SDF File 
Download CCD File 
A
N-(4-{[4-(cyclohexylamino)-1-(3-fluorophenyl)-2-oxo-1,3,8-triazaspiro[4.5]dec-3-en-8-yl]methyl}phenyl)acetamide
C28 H34 F N5 O2
VXIOVOURIXSOTD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SIIIC50: 2800 nM (99) BINDINGDB
SIIIC50: 2800 nM BINDINGMOAD
SIIIC50: 2800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.743α = 90.00
b = 128.042β = 90.00
c = 76.768γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CCP4phasing
HKL-2000data scaling
REFMACrefinement
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-12-17 
  • Released Date: 2009-01-20 
  • Deposition Author(s): Munshi, S.
  • This entry supersedes: 3E3W

Revision History 

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-04-04
    Type: Data collection