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 
  • R-Value Observed: 0.202 

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
  • Primary Citation of Related Structures:  
    3K5C

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1ABC402Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0BI
Query on 0BI

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-diazatric yclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one
C35 H45 N3 O4
GCZHKZTYTMTFGU-JHOUSYSJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0BIIC50 :  17   nM  PDBBind
0BIIC50:  20   nM  BindingDB
0BIIC50:  17   nM  BindingDB
0BIIC50:  17   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.752α = 90
b = 103.186β = 104.44
c = 100.144γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report



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
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description