2VKM

Crystal structure of GRL-8234 bound to BACE (Beta-secretase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Potent Memapsin 2 (Beta-Secretase) Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure, and in Vivo Evaluation.

Ghosh, A.K.Kumaragurubaran, N.Hong, L.Kulkarni, S.Xu, X.Miller, H.B.Reddy, D.S.Weerasena, V.Turner, R.Chang, W.Koelsch, G.Tang, J.

(2008) Bioorg.Med.Chem.Lett. 18: 1031

  • DOI: 10.1016/j.bmcl.2007.12.028

  • PubMed Abstract: 
  • Structure-based design, synthesis, and biological evaluation of a series of peptidomimetic beta-secretase inhibitors incorporating hydroxyethylamine isosteres are described. We have identified inhibitor 24 which has shown exceedingly potent activity ...

    Structure-based design, synthesis, and biological evaluation of a series of peptidomimetic beta-secretase inhibitors incorporating hydroxyethylamine isosteres are described. We have identified inhibitor 24 which has shown exceedingly potent activity in memapsin 2 enzyme inhibitory (K(i) 1.8 nM) and cellular (IC(50)=1 nM in Chinese hamster ovary cells) assays. Inhibitor 24 has also shown very impressive in vivo properties (up to 65% reduction of plasma A beta) in transgenic mice. The X-ray structure of protein-ligand complex of memapsin 2 revealed critical interactions in the memapsin 2 active site.


    Organizational Affiliation

    Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA. akghosh@purdue.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-SECRETASE 1
A, B, C, D
389Homo 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
BSD
Query on BSD

Download SDF File 
Download CCD File 
A, B, C, D
N-{(1S,2R)-1-benzyl-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide
C36 H42 N4 O6 S
HIQWWDCRULXYDF-SWROZOJRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BSDIC50: 1 - 2.5 nM (100) BINDINGDB
BSDKi: 1.8 nM (100) BINDINGDB
BSDKi: 1.8 nM BINDINGMOAD
BSDKi: 1.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.704α = 90.00
b = 130.308β = 97.41
c = 87.711γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance