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

  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1021/ml3001165
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
395Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0V6

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C18 H17 Cl N4 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
0V6 PDBBind:  4FRS Ki: 1.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.473α = 90
b = 89.495β = 90
c = 131.427γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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