3FKT

Crystal Structure of Human Beta Secretase Complexed with Spiropiperdine Iminohydantoin Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.217 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.5 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: https://doi.org/10.1021/jm800914n
  • Primary Citation of Related Structures:  
    3FKT

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1405Homo sapiensMutation(s): 2 
Gene Names: BACEBACE1KIAA1149
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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SII
Query on SII

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
SII BindingDB:  3FKT IC50: 2800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.217 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.743α = 90
b = 128.042β = 90
c = 76.768γ = 90
Software Package:
Software NamePurpose
CCP4model building
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SIIClick on this verticalbar to view details

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-04-04
    Changes: Data collection
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary