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


Ligand Structure Quality Assessment 


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: 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1415Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
EC: 3.4.23.46
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SI5
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
JYDYMWJEZLKIBS-CXMBCZLWSA-N		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A],
I [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SI5 BindingDB:  4XXS IC50: min: 4, max: 52 (nM) from 3 assay(s)
Binding MOAD:  4XXS IC50: 52 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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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