3H0B

Discovery of aminoheterocycles as a novel beta-secretase inhibitor class

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

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This is version 1.2 of the entry. See complete history. 


Literature

Discovery of aminoheterocycles as a novel beta-secretase inhibitor class: pH dependence on binding activity part 1.

Stachel, S.J., Coburn, C.A., Rush, D., Jones, K.L., Zhu, H., Rajapakse, H., Graham, S.L., Simon, A., Katharine Holloway, M., Allison, T.J., Munshi, S.K., Espeseth, A.S., Zuck, P., Colussi, D., Wolfe, A., Pietrak, B.L., Lai, M.T., Vacca, J.P.

(2009) Bioorg Med Chem Lett 19: 2977-2980

  • DOI: 10.1016/j.bmcl.2009.04.033
  • Primary Citation of Related Structures:  
    3H0B

  • PubMed Abstract: 

    • We have developed a novel series of heteroaromatic BACE-1 inhibitors. These inhibitors interact with the enzyme in a unique fashion that allows for potent binding in a non-traditional paradigm. In addition to the elucidation of their binding profile, we have discovered a pH dependent effect on the binding affinity as a result of the intrinsic pK(a) of these inhibitors and the pH of the BACE-1 enzyme binding assay ...

    We have developed a novel series of heteroaromatic BACE-1 inhibitors. These inhibitors interact with the enzyme in a unique fashion that allows for potent binding in a non-traditional paradigm. In addition to the elucidation of their binding profile, we have discovered a pH dependent effect on the binding affinity as a result of the intrinsic pK(a) of these inhibitors and the pH of the BACE-1 enzyme binding assay.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co, West Point, PA 19486, USA. shawn_stachel@merck.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C405Homo sapiensMutation(s): 0 
Gene Names: BACE, BACE1, beta-secretase, 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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B35
Query on B35
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		4-[(1S)-1-(3-fluoro-4-methoxyphenyl)-2-(2-methoxy-5-nitrophenyl)ethyl]-1H-imidazol-2-amine
C19 H19 F N4 O4
RFLOFHKRBGKCOB-AWEZNQCLSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B35 PDBBind:  3H0B IC50: 3200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 221.178α = 90
b = 107.44β = 99.47
c = 65.084γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2009-04-08 
  • Released Date: 2009-07-07 
    • Deposition Author(s): Allison, T.J.

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description