4FSE

crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with N-(N-(4-amino-3,5- dichlorobenzyl)carbamimidoyl)-3-(4-methoxyphenyl)-5- methyl-4-isothiazolecarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Acyl guanidine inhibitors of beta-secretase (BACE-1): optimization of a micromolar hit to a nanomolar lead via iterative solid- and solution-phase library synthesis

Gerritz, S.W.Zhai, W.Shi, S.Zhu, S.Toyn, J.H.Meredith, J.E.Iben, L.G.Burton, C.R.Albright, C.F.Good, A.C.Tebben, A.J.Muckelbauer, J.K.Camac, D.M.Metzler, W.Cook, L.S.Padmanabha, R.Lentz, K.A.Sofia, M.J.Poss, M.A.Macor, J.E.Thompson, L.A.

(2012) J.Med.Chem. 55: 9208-9223

  • DOI: 10.1021/jm300931y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • This report describes the discovery and optimization of a BACE-1 inhibitor series containing an unusual acyl guanidine chemotype that was originally synthesized as part of a 6041-membered solid-phase library. The synthesis of multiple follow-up solid ...

    This report describes the discovery and optimization of a BACE-1 inhibitor series containing an unusual acyl guanidine chemotype that was originally synthesized as part of a 6041-membered solid-phase library. The synthesis of multiple follow-up solid- and solution-phase libraries facilitated the optimization of the original micromolar hit into a single-digit nanomolar BACE-1 inhibitor in both radioligand binding and cell-based functional assay formats. The X-ray structure of representative inhibitors bound to BACE-1 revealed a number of key ligand:protein interactions, including a hydrogen bond between the side chain amide of flap residue Gln73 and the acyl guanidine carbonyl group, and a cation-π interaction between Arg235 and the isothiazole 4-methoxyphenyl substituent. Following subcutaneous administration in rats, an acyl guanidine inhibitor with single-digit nanomolar activity in cells afforded good plasma exposures and a dose-dependent reduction in plasma Aβ levels, but poor brain exposure was observed (likely due to Pgp-mediated efflux), and significant reductions in brain Aβ levels were not obtained.


    Organizational Affiliation

    Bristol-Myers Squibb Research, 5 Research Parkway, Wallingford, Connecticut 06492, United States. samuel.gerritz@bms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B, D, E
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
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, D, E
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
0VA
Query on 0VA

Download SDF File 
Download CCD File 
A, B, D, E
N-[N-(4-amino-3,5-dichlorobenzyl)carbamimidoyl]-3-(4-methoxyphenyl)-5-methyl-1,2-thiazole-4-carboxamide
C20 H19 Cl2 N5 O2 S
DPJQBOWFYJTIJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0VAKi: 40 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.334α = 90.00
b = 131.219β = 97.60
c = 88.947γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-06-27 
  • Released Date: 2012-10-10 
  • Deposition Author(s): Muckelbauer, J.K.

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2018-06-13
    Type: Data collection