3DV1

Crystal structure of human beta-secretase in complex with NVP-ARV999


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 

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.


    Related Citations: 
    • Structure-based design and synthesis of macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors.
      Machauer, R.,Veenstra, S.,Rondeau, J.M.,Tintelnot-Blomley, M.,Betschart, C.,Neumann, U.,Paganetti, P.
      (2009) Bioorg.Med.Chem.Lett. --: --


    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
AR9
Query on AR9

Download SDF File 
Download CCD File 
A, B, C
(2R,4S)-N-butyl-4-[(2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4-diazacyclopentadecan-5-yl]-4-hydroxy-2-methylbutanamide
(2R,4S)-N-Butyl-4-((2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4diaza-cyclopentadec-5-yl)-4-hydroxy-2-methyl-butyramide
C24 H45 N3 O4
ZUIGWVKXPZANDI-MJCUULBUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AR9IC50: 590 - >10000 nM (100) BINDINGDB
AR9IC50: 590 nM BINDINGMOAD
AR9IC50: 590 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.027α = 90.00
b = 102.945β = 103.66
c = 99.916γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
CNSrefinement
MAR345data collection
PDB_EXTRACTdata extraction
CNXrefinement

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