2IRZ

Crystal structure of human Beta-secretase complexed with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of oxadiazoyl tertiary carbinamine inhibitors of beta-secretase (BACE-1).

Rajapakse, H.A.Nantermet, P.G.Selnick, H.G.Munshi, S.McGaughey, G.B.Lindsley, S.R.Young, M.B.Lai, M.T.Espeseth, A.S.Shi, X.P.Colussi, D.Pietrak, B.Crouthamel, M.C.Tugusheva, K.Huang, Q.Xu, M.Simon, A.J.Kuo, L.Hazuda, D.J.Graham, S.Vacca, J.P.

(2006) J.Med.Chem. 49: 7270-7273

  • DOI: 10.1021/jm061046r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the discovery and optimization of tertiary carbinamine derived inhibitors of the enzyme beta-secretase (BACE-1). These novel non-transition-state-derived ligands incorporate a single primary amine to interact with the catalytic aspartates ...

    We describe the discovery and optimization of tertiary carbinamine derived inhibitors of the enzyme beta-secretase (BACE-1). These novel non-transition-state-derived ligands incorporate a single primary amine to interact with the catalytic aspartates of the target enzyme. Optimization of this series provided inhibitors with intrinsic and functional potency comparable to evolved transition state isostere derived inhibitors of BACE-1.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, P.O. Box 4, West Point, Pennsylvania 19486, USA. hemaka_rajapakse@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
I02
Query on I02

Download SDF File 
Download CCD File 
A
3-{5-[(1R)-1-AMINO-1-METHYL-2-PHENYLETHYL]-1,3,4-OXADIAZOL-2-YL}-N-[(1R)-1-(4-FLUOROPHENYL)ETHYL]-5-[METHYL(METHYLSULFONYL)AMINO]BENZAMIDE
C28 H30 F N5 O4 S
QEJSJQVKMSAHHX-KWMCUTETSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I02IC50: 9 - 60 nM (99) BINDINGDB
I02IC50: 12 nM BINDINGMOAD
I02IC50: 12 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 104.530α = 90.00
b = 127.780β = 90.00
c = 76.470γ = 90.00
Software Package:
Software NamePurpose
CNXphasing
HKL-2000data scaling
CNXrefinement
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-10-16 
  • Released Date: 2006-11-14 
  • Deposition Author(s): Munshi, S.

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2007-10-11
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance