3RTN

Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Amino-6-o-tolylquinolin-3-yl)-N-cyclohexylpropanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

From Fragment Screening to In Vivo Efficacy: Optimization of a Series of 2-Aminoquinolines as Potent Inhibitors of Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1).

Cheng, Y.Judd, T.C.Bartberger, M.D.Brown, J.Chen, K.Fremeau, R.T.Hickman, D.Hitchcock, S.A.Jordan, B.Li, V.Lopez, P.Louie, S.W.Luo, Y.Michelsen, K.Nixey, T.Powers, T.S.Rattan, C.Sickmier, E.A.St Jean, D.J.Wahl, R.C.Wen, P.H.Wood, S.

(2011) J.Med.Chem. 54: 5836-5857

  • DOI: 10.1021/jm200544q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Using fragment-based screening of a focused fragment library, 2-aminoquinoline 1 was identified as an initial hit for BACE1. Further SAR development was supported by X-ray structures of BACE1 cocrystallized with various ligands and molecular modeling ...

    Using fragment-based screening of a focused fragment library, 2-aminoquinoline 1 was identified as an initial hit for BACE1. Further SAR development was supported by X-ray structures of BACE1 cocrystallized with various ligands and molecular modeling studies to expedite the discovery of potent compounds. These strategies enabled us to integrate the C-3 side chain on 2-aminoquinoline 1 extending deep into the P2' binding pocket of BACE1 and enhancing the ligand's potency. We were able to improve the BACE1 potency to subnanomolar range, over 10(6)-fold more potent than the initial hit (900 μM). Further elaboration of the physical properties of the lead compounds to those more consistent with good blood-brain barrier permeability led to inhibitors with greatly improved cellular activity and permeability. Compound 59 showed an IC(50) value of 11 nM on BACE1 and cellular activity of 80 nM. This compound was advanced into rat pharmacokinetic and pharmacodynamic studies and demonstrated significant reduction of Aβ levels in cerebrospinal fluid (CSF).


    Organizational Affiliation

    Chemistry Research and Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, USA. yuanc@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
411Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTN
Query on RTN

Download SDF File 
Download CCD File 
A
3-[2-amino-6-(2-methylphenyl)quinolin-3-yl]-N-cyclohexylpropanamide
C25 H29 N3 O
JBOWUKRDBGMOJZ-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RTNIC50: 74 nM (99) BINDINGDB
RTNIC50: 74 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 103.365α = 90.00
b = 103.365β = 90.00
c = 170.197γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-05-03 
  • Released Date: 2011-08-31 
  • Deposition Author(s): Sickmier, E.A.

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release