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: 1.70 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. 


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
  • Primary Citation of Related Structures:  
    4FRS

  • 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 subs ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1 A, B395Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS:  P56817
GTEx:  ENSG00000186318
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0V6
Query on 0V6
Download Ideal Coordinates 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 :  1.7000000476837158   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

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
    Changes: Non-polymer description
  • Version 1.2: 2013-06-19
    Changes: Database references