3DUY

Crystal structure of human beta-secretase in complex with NVP-AFJ144


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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 19: 1361-1365

  • DOI: 10.1016/j.bmcl.2009.01.036
  • Primary Citation of Related Structures:  
    3DUY

  • PubMed Abstract: 
  • The hydroxyethylene octapeptide inhibitor OM99-2 served as starting point to create the tripeptide inhibitor 1 and its analogues 2a and b. An X-ray co-crystal structure of 1 with BACE-1 allowed the design and syntheses of a series of macrocyclic anal ...

    The hydroxyethylene octapeptide inhibitor OM99-2 served as starting point to create the tripeptide inhibitor 1 and its analogues 2a and b. An X-ray co-crystal structure of 1 with BACE-1 allowed the design and syntheses of a series of macrocyclic analogues 3a-h covalently linking the P1 and P3 side-chains. These inhibitors show improved enzymatic potency over their open-chain analogue. Inhibitor 3h also shows activity in a cellular system.


    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 1ABC402Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AFJ
Query on AFJ

Download CCD File 
A, B, C
(2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide
C25 H49 N3 O4 S
XTRMRNMVFXWTCC-MLNNCEHLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AFJIC50:  10000   nM  BindingDB
AFJIC50 :  1400   nM  PDBBind
AFJIC50:  1400   nM  Binding MOAD
AFJIC50:  1400   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.537α = 90
b = 103.062β = 103.64
c = 100.602γ = 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: 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
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description