3DV5

Crystal structure of human beta-secretase in complex with NVP-BAV544


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1366-1370

  • DOI: 10.1016/j.bmcl.2009.01.055
  • Primary Citation of Related Structures:  
  • Also Cited By: 3PI5

  • PubMed Abstract: 
  • The macrocyclic peptidic BACE-1 inhibitors 2a-c show moderate enzymatic and cellular activity. By exchange of the hydroxyethylene- to ethanolamine-transition state mimetic the peptidic character was reduced, providing the highly potent and selective ...

    The macrocyclic peptidic BACE-1 inhibitors 2a-c show moderate enzymatic and cellular activity. By exchange of the hydroxyethylene- to ethanolamine-transition state mimetic the peptidic character was reduced, providing the highly potent and selective inhibitor 3. Variation of the P' moiety resulted in the macrocyclic inhibitor 14. Both macrocycles show inhibition of BACE-1 in the brain of APP51/16 transgenic mice, 3 (NB-544) after intravenous and 14 (NB-533) after oral application.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Pharma AG, PO Box, CH-4002 Basel, Switzerland.




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
BAV
Query on BAV

Download SDF File 
Download CCD File 
A, B, C
(3S,14R,16S)-16-[(1R)-1-hydroxy-2-{[3-(1-methylethyl)benzyl]amino}ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5-dione
(3S,14R,16S)-16-[(R)-1-Hydroxy-2-(3-isopropyl-benzylamino)-ethyl]-3,4,14-trimethyl-1,4diaza-cyclohexadecane-2,5-dione
C29 H49 N3 O3
LHBBUGLYVFZUTH-GXVHRJHYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BAVIC50: 27 - 45 nM (100) BINDINGDB
BAVIC50: 27 nM BINDINGMOAD
BAVIC50: 22 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.661α = 90.00
b = 103.353β = 103.72
c = 99.474γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAR345data collection
CNSrefinement
CNXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-07-18 
  • Released Date: 2009-02-24 
  • Deposition Author(s): Rondeau, J.-M.

Revision History 

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description