3IVI

Design and Synthesis of Potent BACE-1 Inhibitors with Cellular Activity: Structure-Activity Relationship of P1 Substituents


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design and synthesis of cell potent BACE-1 inhibitors: structure-activity relationship of P1' substituents.

Sealy, J.M.Truong, A.P.Tso, L.Probst, G.D.Aquino, J.Hom, R.K.Jagodzinska, B.M.Dressen, D.Wone, D.W.Brogley, L.John, V.Tung, J.S.Pleiss, M.A.Tucker, J.A.Konradi, A.W.Dappen, M.S.Toth, G.Pan, H.Ruslim, L.Miller, J.Bova, M.P.Sinha, S.Quinn, K.P.Sauer, J.M.

(2009) Bioorg Med Chem Lett 19: 6386-6391

  • DOI: 10.1016/j.bmcl.2009.09.061
  • Primary Citation of Related Structures:  
    3IVH, 3IVI

  • PubMed Abstract: 
  • Using structure-guided design, hydroxyethylamine BACE-1 inhibitors were optimized to nanomolar Abeta cellular inhibition with selectivity against cathepsin-D. X-ray crystallography illuminated the S1' residues critical to this effort, which culminate ...

    Using structure-guided design, hydroxyethylamine BACE-1 inhibitors were optimized to nanomolar Abeta cellular inhibition with selectivity against cathepsin-D. X-ray crystallography illuminated the S1' residues critical to this effort, which culminated in compounds 56 and 57 that exhibited potency and selectivity but poor permeability and high P-gp efflux.


    Organizational Affiliation

    Department of Medicinal Chemistry, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1ABC406Homo 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2LI
Query on 2LI

Download CCD File 
A, B, C
N-[(1S,2R)-3-{[(5S)-5-(3-tert-butylphenyl)-4,5,6,7-tetrahydro-1H-indazol-5-yl]amino}-1-(3,5-difluorobenzyl)-2-hydroxypropyl]acetamide
C29 H36 F2 N4 O2
BAILJXDQIBWAPX-GKRYNVPLSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2LIIC50:  12   nM  Binding MOAD
2LIIC50:  12   nM  BindingDB
2LIIC50 :  12   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.711α = 90
b = 104.48β = 104.83
c = 100.616γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-09-01 
  • Released Date: 2010-01-05 
  • Deposition Author(s): Pan, H.

Revision History 

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance