3K5C

Human BACE-1 complex with NB-216


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Macrocyclic BACE-1 inhibitors acutely reduce Abeta in brain after po application.

Lerchner, A.Machauer, R.Betschart, C.Veenstra, S.Rueeger, H.McCarthy, C.Tintelnot-Blomley, M.Jaton, A.L.Rabe, S.Desrayaud, S.Enz, A.Staufenbiel, M.Paganetti, P.Rondeau, J.M.Neumann, U.

(2010) Bioorg.Med.Chem.Lett. 20: 603-607

  • DOI: 10.1016/j.bmcl.2009.11.092

  • PubMed Abstract: 
  • A series of macrocyclic peptidic BACE-1 inhibitors was designed. While potency on BACE-1 was rather high, the first set of compounds showed poor brain permeation and high efflux in the MDRI-MDCK assay. The replacement of the secondary benzylamino gro ...

    A series of macrocyclic peptidic BACE-1 inhibitors was designed. While potency on BACE-1 was rather high, the first set of compounds showed poor brain permeation and high efflux in the MDRI-MDCK assay. The replacement of the secondary benzylamino group with a phenylcyclopropylamino group maintained potency on BACE-1, while P-glycoprotein-mediated efflux was significantly reduced and brain permeation improved. Several compounds from this series demonstrated acute reduction of Abeta in human APP-wildtype transgenic (APP51/16) mice after oral administration.


    Related Citations: 
    • Macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors with activity in vivo
      Machauer, R.,Laumen, K.,Veenstra, S.,Rondeau, J.-M.,Tintelnot-Blomley, M.,Betschart, C.,Jaton, A.-L.,Desrayaud, S.,Staufenbiel, M.,Rabe, S.,Paganetti, P.,Neumann, U.
      (2009) Bioorg. Med. Chem. Lett. 19: 1366


    Organizational Affiliation

    Novartis Institutes for BioMedicalResearch, Novartis Pharma AG, PO Box, CH 4002, Basel, Switzerland. andreas.lerchner@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B, C
402Homo sapiensMutation(s): 0 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0BI
Query on 0BI

Download SDF File 
Download CCD File 
A, B, C
(4S)-4-[(1R)-1-hydroxy-2-({1-[3-(1-methylethyl)phenyl]cyclopropyl}amino)ethyl]-19-(methoxymethyl)-11-oxa-3,16-diazatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one
(S)-4-{(R)-1-Hydroxy-2-[1-(3-isopropyl-phenyl)-cyclopropylamino]-ethyl}-19-methoxymethyl-11-oxa 3,16-diaza-tricyclo[15.3.1.1*6,10*]docosa-1(21),6,8,10(22),17 ,19-hexaen-2-one
C35 H45 N3 O4
GCZHKZTYTMTFGU-JHOUSYSJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0BIIC50: 17 - 20 nM (100) BINDINGDB
0BIIC50: 17 nM BINDINGMOAD
0BIIC50: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.752α = 90.00
b = 103.186β = 104.44
c = 100.144γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNXphasing
XDSdata reduction
CNXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-10-07 
  • Released Date: 2010-03-02 
  • Deposition Author(s): Rondeau, J.-M.

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description