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 

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
  • Also Cited By: 3PI5, 3DV1

  • 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: 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
AFJ
Query on AFJ

Download SDF File 
Download CCD File 
A, B, C
(2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide
(2R,4S,5S)-4-Hydroxy-2,7-dimethyl-5-[(S)-2-(4-methyl-pentanoylamino)-4-methylsulfanyl-butyrylamino]-octanoic acid butylamide
C25 H49 N3 O4 S
XTRMRNMVFXWTCC-MLNNCEHLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AFJIC50: 1400 - >10000 nM (100) BINDINGDB
AFJIC50: 1400 nM BINDINGMOAD
AFJIC50: 1400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.537α = 90.00
b = 103.062β = 103.64
c = 100.602γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
CNSrefinement
CNXphasing
XSCALEdata scaling

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