3K5F

Human BACE-1 COMPLEX WITH AYH011


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based design and synthesis of novel P2/P3 modified, non-peptidic beta-secretase (BACE-1) inhibitors.

Hanessian, S.Shao, Z.Betschart, C.Rondeau, J.M.Neumann, U.Tintelnot-Blomley, M.

(2010) Bioorg.Med.Chem.Lett. 20: 1924-1927

  • DOI: 10.1016/j.bmcl.2010.01.139
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Starting from peptidomimetic BACE-1 inhibitors, the P2 amino acid including the P2/P3 peptide bond was replaced by a rigid 3-aminomethyl cyclohexane carboxylic acid. Co-crystallization revealed an unexpected binding mode with the P3/P4 amide bond pla ...

    Starting from peptidomimetic BACE-1 inhibitors, the P2 amino acid including the P2/P3 peptide bond was replaced by a rigid 3-aminomethyl cyclohexane carboxylic acid. Co-crystallization revealed an unexpected binding mode with the P3/P4 amide bond placed into the S3 pocket resulting in a new hydrogen bond interaction pattern. Further optimization based on this structure resulted in highly potent BACE-1 inhibitors with selectivity over BACE-2 and cathepsin D.


    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. 19: 1361
    • 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


    Organizational Affiliation

    Department of Chemistry, Université de Montréal, Montréal, Canada. stephen.hanessian@umontreal.ca




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
AYH
Query on AYH

Download SDF File 
Download CCD File 
A, B, C
(1R,3S)-3-[1-(acetylamino)-1-methylethyl]-N-[(1S,2S,4R)-1-benzyl-5-(butylamino)-2-hydroxy-4-methyl-5-oxopentyl]cyclohexanecarboxamide
(1R,3S)-3-(1-Acetylamino-1-methyl-ethyl)-cyclohexanecarboxylic acid ((1S,2S,4R)-1-benzyl-4-butylcarbamoyl-2-hydroxy-pentyl)-amide
C29 H47 N3 O4
NGUMIHCAWWHVPZ-MTKOPPBXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AYHIC50: 3700 nM (100) BINDINGDB
AYHIC50: 3700 nM BINDINGMOAD
AYHIC50: 3700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.651α = 90.00
b = 103.708β = 102.53
c = 101.818γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNXrefinement
CNXphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-10-07 
  • Released Date: 2010-05-05 
  • Deposition Author(s): Rondeau, J.-M.

Revision History 

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description