4FRS

Structure of BACE in complex with (S)-4-(3-chloro-5-(5-(prop-1-yn-1-yl)pyridin-3-yl)thiophen-2-yl)-1,4-dimethyl-6-oxotetrahydropyrimidin-2(1H)-iminium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of an Orally Available, Brain Penetrant BACE1 Inhibitor That Affords Robust CNS A(beta) Reduction

Stamford, A.W.Scott, J.D.Li, S.W.Babu, S.Tadesse, D.Hunter, R.Wu, Y.Misiaszek, J.Cumming, J.N.Gilbert, E.J.Huang, C.McKittrick, B.A.Hong, L.Guo, T.Zhu, Z.Strickland, C.Orth, P.Voigt, J.H.Kennedy, M.E.Chen, X.Kuvelkar, R.Hodgson, R.Hyde, L.A.Cox, K.Favreau, L.Parker, E.M.Greenlee, W.J.

(2012) ACS Med Chem Lett 3: 897-902

  • DOI: 10.1021/ml3001165

  • PubMed Abstract: 
  • Inhibition of BACE1 to prevent brain Aβ peptide formation is a potential disease-modifying approach to the treatment of Alzheimer's disease. Despite over a decade of drug discovery efforts, the identification of brain-penetrant BACE1 inhibitors that ...

    Inhibition of BACE1 to prevent brain Aβ peptide formation is a potential disease-modifying approach to the treatment of Alzheimer's disease. Despite over a decade of drug discovery efforts, the identification of brain-penetrant BACE1 inhibitors that substantially lower CNS Aβ levels following systemic administration remains challenging. In this report we describe structure-based optimization of a series of brain-penetrant BACE1 inhibitors derived from an iminopyrimidinone scaffold. Application of structure-based design in tandem with control of physicochemical properties culminated in the discovery of compound 16, which potently reduced cortex and CSF Aβ40 levels when administered orally to rats.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B
395Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0V6
Query on 0V6

Download SDF File 
Download CCD File 
A, B
(2Z,6S)-6-{3-chloro-5-[5-(prop-1-yn-1-yl)pyridin-3-yl]thiophen-2-yl}-2-imino-3,6-dimethyltetrahydropyrimidin-4(1H)-one
C18 H17 Cl N4 O S
IJYPXSRDUPWKPB-SFHVURJKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0V6Ki: 1.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.473α = 90.00
b = 89.495β = 90.00
c = 131.427γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTERrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-06-26 
  • Released Date: 2012-08-08 
  • Deposition Author(s): Orth, P.

Revision History 

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-11-21
    Type: Non-polymer description
  • Version 1.2: 2013-06-19
    Type: Database references