5HDV

BACE-1 incomplex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methoxy-6-methylpyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of an Iminoheterocyclic beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central A beta in Nonhuman Primates.

Mandal, M.Wu, Y.Misiaszek, J.Li, G.Buevich, A.Caldwell, J.P.Liu, X.Mazzola, R.D.Orth, P.Strickland, C.Voigt, J.Wang, H.Zhu, Z.Chen, X.Grzelak, M.Hyde, L.A.Kuvelkar, R.Leach, P.T.Terracina, G.Zhang, L.Zhang, Q.Michener, M.S.Smith, B.Cox, K.Grotz, D.Favreau, L.Mitra, K.Kazakevich, I.McKittrick, B.A.Greenlee, W.Kennedy, M.E.Parker, E.M.Cumming, J.N.Stamford, A.W.

(2016) J.Med.Chem. 59: 3231-3248

  • DOI: 10.1021/acs.jmedchem.5b01995
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure- ...

    We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure-based design, truncation of the cyanophenyl group of 6 that binds in the S3 pocket of BACE1 followed by modification of the thienyl group in S1 was pursued. Optimization of the pyrimidine substituent that binds in the S2'-S2″ pocket of BACE1 remediated time-dependent CYP3A4 inhibition of earlier analogues in this series and imparted high BACE1 affinity. These efforts resulted in the discovery of difluorophenyl analogue 9 (MBi-4), which robustly lowered CSF and cortex Aβ40 in both rats and cynomolgus monkeys following a single oral dose. Compound 9 represents a unique molecular shape among BACE inhibitors reported to potently lower central Aβ in nonrodent preclinical species.


    Organizational Affiliation

    Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B
414Homo 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
60V
Query on 60V

Download SDF File 
Download CCD File 
A, B
5-[(2E,4aR,7aR)-6-(5-fluoro-4-methoxy-6-methylpyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophene-2-carbonitrile
C18 H18 F N7 O2 S
ZPAVWCJTQRQRQL-VOJFVSQTSA-N
 Ligand Interaction
TLA
Query on TLA

Download SDF File 
Download CCD File 
B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.410α = 90.00
b = 89.320β = 90.00
c = 131.280γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-01-05 
  • Released Date: 2016-03-16 
  • Deposition Author(s): Orth, P.

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references