4XXS

Crystal structure of BACE1 with a pyrazole-substituted tetrahydropyran thioamidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Utilizing Structures of CYP2D6 and BACE1 Complexes To Reduce Risk of Drug-Drug Interactions with a Novel Series of Centrally Efficacious BACE1 Inhibitors.

Brodney, M.A.Beck, E.M.Butler, C.R.Barreiro, G.Johnson, E.F.Riddell, D.Parris, K.Nolan, C.E.Fan, Y.Atchison, K.Gonzales, C.Robshaw, A.E.Doran, S.D.Bundesmann, M.W.Buzon, L.Dutra, J.Henegar, K.LaChapelle, E.Hou, X.Rogers, B.N.Pandit, J.Lira, R.Martinez-Alsina, L.Mikochik, P.Murray, J.C.Ogilvie, K.Price, L.Sakya, S.M.Yu, A.Zhang, Y.O'Neill, B.T.

(2015) J Med Chem 58: 3223-3252

  • DOI: 10.1021/acs.jmedchem.5b00191
  • Primary Citation of Related Structures:  
    4XRY, 4XRZ, 4XXS

  • PubMed Abstract: 
  • In recent years, the first generation of β-secretase (BACE1) inhibitors advanced into clinical development for the treatment of Alzheimer's disease (AD). However, the alignment of drug-like properties and selectivity remains a major challenge. Herein ...

    In recent years, the first generation of β-secretase (BACE1) inhibitors advanced into clinical development for the treatment of Alzheimer's disease (AD). However, the alignment of drug-like properties and selectivity remains a major challenge. Herein, we describe the discovery of a novel class of potent, low clearance, CNS penetrant BACE1 inhibitors represented by thioamidine 5. Further profiling suggested that a high fraction of the metabolism (>95%) was due to CYP2D6, increasing the potential risk for victim-based drug-drug interactions (DDI) and variable exposure in the clinic due to the polymorphic nature of this enzyme. To guide future design, we solved crystal structures of CYP2D6 complexes with substrate 5 and its corresponding metabolic product pyrazole 6, which provided insight into the binding mode and movements between substrate/inhibitor complexes. Guided by the BACE1 and CYP2D6 crystal structures, we designed and synthesized analogues with reduced risk for DDI, central efficacy, and improved hERG therapeutic margins.


    Organizational Affiliation

    ∇WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A415Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SI5
Query on SI5

Download CCD File 
A
(4aR,6R,8aS)-8a-(2,4-difluorophenyl)-6-(1-methyl-1H-pyrazol-4-yl)-4,4a,5,6,8,8a-hexahydropyrano[3,4-d][1,3]thiazin-2-amine
C17 H18 F2 N4 O S
JYDYMWJEZLKIBS-CXMBCZLWSA-N
 Ligand Interaction
IOD
Query on IOD

Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SI5IC50:  52   nM  BindingDB
SI5IC50:  4   nM  BindingDB
SI5IC50:  39.79999923706055   nM  BindingDB
SI5IC50:  52   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.35α = 90
b = 102.35β = 90
c = 170.55γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
BUSTER-TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references