5I3V

Crystal structure of BACE1 in complex with aminoquinoline compound 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Fragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of beta-Secretase.

Jordan, J.B., Whittington, D.A., Bartberger, M.D., Sickmier, E.A., Chen, K., Cheng, Y., Judd, T.

(2016) J Med Chem 59: 3732-3749

  • DOI: 10.1021/acs.jmedchem.5b01917
  • Primary Citation of Related Structures:  
    5I3V, 5I3W, 5I3X, 5I3Y, 5IE1

  • PubMed Abstract: 

    • Fragment-based drug discovery (FBDD) has become a widely used tool in small-molecule drug discovery efforts. One of the most commonly used biophysical methods in detecting weak binding of fragments is nuclear magnetic resonance (NMR) spectroscopy. In particular, FBDD performed with (19)F NMR-based methods has been shown to provide several advantages over (1)H NMR using traditional magnetization-transfer and/or two-dimensional methods ...

    Fragment-based drug discovery (FBDD) has become a widely used tool in small-molecule drug discovery efforts. One of the most commonly used biophysical methods in detecting weak binding of fragments is nuclear magnetic resonance (NMR) spectroscopy. In particular, FBDD performed with (19)F NMR-based methods has been shown to provide several advantages over (1)H NMR using traditional magnetization-transfer and/or two-dimensional methods. Here, we demonstrate the utility and power of (19)F-based fragment screening by detailing the identification of a second-site fragment through (19)F NMR screening that binds to a specific pocket of the aspartic acid protease, β-secretase (BACE-1). The identification of this second-site fragment allowed the undertaking of a fragment-linking approach, which ultimately yielded a molecule exhibiting a more than 360-fold increase in potency while maintaining reasonable ligand efficiency and gaining much improved selectivity over cathepsin-D (CatD). X-ray crystallographic studies of the molecules demonstrated that the linked fragments exhibited binding modes consistent with those predicted from the targeted screening approach, through-space NMR data, and molecular modeling.

    Organizational Affiliation: 

    Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, California 91320, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A411Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
68M
Query on 68M
Download Ideal Coordinates CCD File 
E [auth A](2R)-3-[2-amino-6-(3-methylpyridin-2-yl)quinolin-3-yl]-N-(3,3-dimethylbutyl)-2-methylpropanamide
C25 H32 N4 O
ZVOWIRUWKAUSAB-QGZVFWFLSA-N		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
68M Binding MOAD:  5I3V Kd: 16 (nM) from 1 assay(s)
BindingDB:  5I3V IC50: min: 16, max: 35 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.953α = 90
b = 102.953β = 90
c = 170.381γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2016-05-11
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations