4FSL

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.4 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:  
    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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A,
B,
C [auth D],
D [auth E]		412Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0VB
Query on 0VB
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth D],
Q [auth E]		N-{N-[4-(acetylamino)-3-chloro-5-methylbenzyl]carbamimidoyl}-3-(4-methoxyphenyl)-5-methyl-1,2-thiazole-4-carboxamide
C23 H24 Cl N5 O3 S
MQPJKTGBSCCWTI-UHFFFAOYSA-N		 Ligand Interaction
IOD
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]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0VB PDBBind:  4FSL Ki: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

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