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 1.4 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: https://doi.org/10.1021/jm061046r
  • Primary Citation of Related Structures:  
    2IRZ, 2IS0

  • 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 of the target enzyme ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1405Homo sapiensMutation(s): 2 
Gene Names: BACE1, BACE, KIAA1149
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I02
Query on I02
Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
I02 BindingDB:  2IRZ IC50: min: 9, max: 60 (nM) from 3 assay(s)
Binding MOAD:  2IRZ IC50: 12 (nM) from 1 assay(s)
PDBBind:  2IRZ IC50: 12 (nM) from 1 assay(s)
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



View more in-depth experimental data
Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description