Crystal structure of BACE1 with a pyrazole-substituted tetrahydropyran thioamidine

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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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: https://doi.org/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, 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

    #The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92024, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1415Homo 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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SI5

Download Ideal Coordinates CCD File 
B [auth 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
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth A]
C3 H8 O3
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
SI5 Binding MOAD:  4XXS IC50: 52 (nM) from 1 assay(s)
BindingDB:  4XXS IC50: min: 4, max: 52 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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