4FS4

Structure of BACE Bound to (S)-4-(3'-methoxy-[1,1'-biphenyl]-3-yl)-1,4-dimethyl-6-oxotetrahydropyrimidin-2(1H)-iminium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Potent and Orally Efficacious, Hydroxyethylamine-Based Inhibitor of beta-Secretase.

Kaller, M.R.Harried, S.S.Albrecht, B.Amarante, P.Babu-Khan, S.Bartberger, M.D.Brown, J.Brown, R.Chen, K.Cheng, Y.Citron, M.Croghan, M.D.Graceffa, R.Hickman, D.Judd, T.Kriemen, C.La, D.Li, V.Lopez, P.Luo, Y.Masse, C.Monenschein, H.Nguyen, T.Pennington, L.D.Miguel, T.S.Sickmier, E.A.Wahl, R.C.Weiss, M.M.Wen, P.H.Williamson, T.Wood, S.Xue, M.Yang, B.Zhang, J.Patel, V.Zhong, W.Hitchcock, S.

(2012) ACS Med Chem Lett 3: 886-891

  • DOI: 10.1021/ml3000148
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • β-Secretase inhibitors are potentially disease-modifying treatments for Alzheimer's disease. Previous efforts in our laboratory have resulted in hydroxyethylamine-derived inhibitors such as 1 with low nanomolar potency against β-site amyloid precurso ...

    β-Secretase inhibitors are potentially disease-modifying treatments for Alzheimer's disease. Previous efforts in our laboratory have resulted in hydroxyethylamine-derived inhibitors such as 1 with low nanomolar potency against β-site amyloid precursor protein cleaving enzyme (BACE). When dosed intravenously, compound 1 was also shown to significantly reduce Aβ40 levels in plasma, brain, and cerebral spinal fluid. Herein, we report further optimizations that led to the discovery of inhibitor 16 as a novel, potent, and orally efficacious BACE inhibitor.


    Organizational Affiliation

    Chemistry Research and Discovery, Department of Molecular Structure, Department of Neuroscience, Department of HTS and Molecular Pharmacology, and Department of Pharmacokinetics and Drug Metabolism, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B
390Homo 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
H24
Query on H24

Download SDF File 
Download CCD File 
A, B
(6S)-2-amino-6-(3'-methoxybiphenyl-3-yl)-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one
C19 H21 N3 O2
LQOCXPOKEPYGTJ-IBGZPJMESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
H24IC50: 380 - 91000 nM (100) BINDINGDB
H24Ki: 270 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.500α = 90.00
b = 90.364β = 90.00
c = 131.146γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
StructureStudiodata collection
SCALEPACKdata scaling
BUSTER-TNTrefinement
CNXphasing
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2014-07-23
    Type: Database references