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 
  • R-Value Observed: 0.207 

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:  
    4DUS, 4FS4

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1AB390Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H24
Query on H24

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
TLA
Query on TLA

Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
H24IC50:  590   nM  BindingDB
H24Ki :  270   nM  PDBBind
H24IC50:  91000   nM  BindingDB
H24IC50:  670   nM  BindingDB
H24IC50:  380   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.5α = 90
b = 90.364β = 90
c = 131.146γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
CNXphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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