Crystal structure of beta-site app-cleaving enzyme 1 (BACE-DB-MUT) complex with N-(N-(4- acetamido-3-chloro-5-methylbenzyl)carbamimidoyl)-3-(4- methoxyphenyl)-5-methyl-4-isothiazolecarboxamide

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1021/jm300931y
  • Primary Citation of Related Structures:  
    4FSE, 4FSL

  • 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- 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1A,
C [auth D],
D [auth E]
412Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0VB

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth D],
Q [auth E]
C23 H24 Cl N5 O3 S
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth D],
O [auth D],
P [auth D],
R [auth E],
S [auth E],
T [auth E]
Binding Affinity Annotations 
IDSourceBinding Affinity
0VB PDBBind:  4FSL Ki: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.54α = 90
b = 131.177β = 97.61
c = 90.315γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2018-06-13
    Changes: Data collection
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description