2IRZ

Crystal structure of human Beta-secretase complexed with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.219 
  • R-Value Observed: 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:  
    2IS0, 2IRZ

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A405Homo sapiensMutation(s): 2 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I02
Query on I02

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   nM  BindingDB
I02IC50 :  12   nM  PDBBind
I02IC50:  12   nM  Binding MOAD
I02IC50:  12   nM  BindingDB
I02IC50:  60   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.53α = 90
b = 127.78β = 90
c = 76.47γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNXphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance