4DH6

Structure of Bace-1 (Beta-Secretase) in Complex with (2R)-N-((2S,3R)-1-(benzo[d][1,3]dioxol-5-yl)-3-hydroxy-4-((S)-6'-neopentyl-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridine]-4'-ylamino)butan-2-yl)-2-methoxypropanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and preparation of a potent series of hydroxyethylamine containing beta-secretase inhibitors that demonstrate robust reduction of central beta-amyloid.

Weiss, M.M.Williamson, T.Babu-Khan, S.Bartberger, M.D.Brown, J.Chen, K.Cheng, Y.Citron, M.Croghan, M.D.Dineen, T.A.Esmay, J.Graceffa, R.F.Harried, S.S.Hickman, D.Hitchcock, S.A.Horne, D.B.Huang, H.Imbeah-Ampiah, R.Judd, T.Kaller, M.R.Kreiman, C.R.La, D.S.Li, V.Lopez, P.Louie, S.Monenschein, H.Nguyen, T.T.Pennington, L.D.Rattan, C.San Miguel, T.Sickmier, E.A.Wahl, R.C.Wen, P.H.Wood, S.Xue, Q.Yang, B.H.Patel, V.F.Zhong, W.

(2012) J.Med.Chem. 55: 9009-9024

  • DOI: 10.1021/jm300119p

  • PubMed Abstract: 
  • A series of potent hydroxyethyl amine (HEA) derived inhibitors of β-site APP cleaving enzyme (BACE1) was optimized to address suboptimal pharmacokinetics and poor CNS partitioning. This work identified a series of benzodioxolane analogues that posses ...

    A series of potent hydroxyethyl amine (HEA) derived inhibitors of β-site APP cleaving enzyme (BACE1) was optimized to address suboptimal pharmacokinetics and poor CNS partitioning. This work identified a series of benzodioxolane analogues that possessed improved metabolic stability and increased oral bioavailability. Subsequent efforts focused on improving CNS exposure by limiting susceptibility to Pgp-mediated efflux and identified an inhibitor which demonstrated robust and sustained reduction of CNS β-amyloid (Aβ) in Sprague-Dawley rats following oral administration.


    Organizational Affiliation

    Department of Chemistry Research and Discovery, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States. mmweiss@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
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
0KN
Query on 0KN

Download SDF File 
Download CCD File 
A
(2R)-N-[(2S,3R)-1-(1,3-benzodioxol-5-yl)-4-{[(4'S)-6'-(2,2-dimethylpropyl)-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridin]-4'-yl]amino}-3-hydroxybutan-2-yl]-2-methoxypropanamide
(2R)-N-((2S,3R)-1-(benzo[d][1,3]dioxol-5-yl)-3-hydroxy-4-((S)-6'-neopentyl-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridine]-4'-ylamino)butan-2-yl)-2-methoxypropanamide
C31 H43 N3 O6
OMMVFRZSBCRMQD-LJYZBVLISA-N
 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 %)
0KNIC50: 14 - 26 nM (99) BINDINGDB
0KNIC50: 16.8 nM BINDINGMOAD
0KNIC50: 16.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.226 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 103.694α = 90.00
b = 103.694β = 90.00
c = 168.866γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-01-27 
  • Released Date: 2012-04-18 
  • Deposition Author(s): Sickmier, E.A.

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references