3DV1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    3DV1, 3DV5

  • 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 inhibitor 3 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C402Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR9 (Subject of Investigation/LOI)
Query on AR9

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C](2R,4S)-N-butyl-4-[(2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4-diazacyclopentadecan-5-yl]-4-hydroxy-2-methylbutanamide
C24 H45 N3 O4
ZUIGWVKXPZANDI-MJCUULBUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AR9 BindingDB:  3DV1 IC50: min: 590, max: 1.00e+4 (nM) from 2 assay(s)
Binding MOAD:  3DV1 IC50: 590 (nM) from 1 assay(s)
PDBBind:  3DV1 IC50: 590 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.027α = 90
b = 102.945β = 103.66
c = 99.916γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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