3LPK

Structure of BACE Bound to SCH747123


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Piperazine sulfonamide BACE1 inhibitors: design, synthesis, and in vivo characterization.

Cumming, J.Babu, S.Huang, Y.Carrol, C.Chen, X.Favreau, L.Greenlee, W.Guo, T.Kennedy, M.Kuvelkar, R.Le, T.Li, G.McHugh, N.Orth, P.Ozgur, L.Parker, E.Saionz, K.Stamford, A.Strickland, C.Tadesse, D.Voigt, J.Zhang, L.Zhang, Q.

(2010) Bioorg.Med.Chem.Lett. 20: 2837-2842

  • DOI: 10.1016/j.bmcl.2010.03.050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • With collaboration between chemistry, X-ray crystallography, and molecular modeling, we designed and synthesized a series of novel piperazine sulfonamide BACE1 inhibitors. Iterative exploration of the non-prime side and S2' sub-pocket of the enzyme c ...

    With collaboration between chemistry, X-ray crystallography, and molecular modeling, we designed and synthesized a series of novel piperazine sulfonamide BACE1 inhibitors. Iterative exploration of the non-prime side and S2' sub-pocket of the enzyme culminated in identification of an analog that potently lowers peripheral Abeta(40) in transgenic mice with a single subcutaneous dose.


    Organizational Affiliation

    Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. jared.cumming@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B
455Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download SDF File 
Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Z76
Query on Z76

Download SDF File 
Download CCD File 
A, B
N-[(1S,2S)-1-(3,5-difluorobenzyl)-2-hydroxy-2-{(2R)-4-[(3-methylphenyl)sulfonyl]piperazin-2-yl}ethyl]-3-{[(2R)-2-(methoxymethyl)pyrrolidin-1-yl]carbonyl}-5-methylbenzamide
C35 H42 F2 N4 O6 S
CQQMWBPWYUPVOC-PPESYSCFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Z76IC50: 7 nM (100) BINDINGDB
Z76Ki: 0.8 nM (100) BINDINGDB
Z76Ki: 0.8 nM BINDINGMOAD
Z76Ki: 0.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.511α = 90.00
b = 89.934β = 90.00
c = 131.145γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description