4D8C

Crystal Structure of Human Beta Secretase in Complex with NVP-BXD552, derived from a co-crystallization experiment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


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Literature

Discovery of cyclic sulfone hydroxyethylamines as potent and selective beta-site APP-cleaving enzyme 1 (BACE1) inhibitors: structure based design and in vivo reduction of amyloid beta-peptides

Rueeger, H., Lueoend, R., Rogel, O., Rondeau, J.M., Mobitz, H., Machauer, R., Jacobson, L., Staufenbiel, M., Desrayaud, S., Neumann, U.

(2012) J Med Chem 55: 3364-3386

  • DOI: 10.1021/jm300069y
  • Primary Citation of Related Structures:  
    3VEU, 3VF3, 3VG1, 4D83, 4D85, 4D88, 4D89, 4D8C

  • PubMed Abstract: 

    • Structure-based design of a series of cyclic hydroxyethylamine BACE1 inhibitors allowed the rational incorporation of prime- and nonprime-side fragments to a central core template without any amide functionality. The core scaffold selection and the structure-activity relationship development were supported by molecular modeling studies and by X-ray analysis of BACE1 complexes with various ligands to expedite the optimization of the series ...

    Structure-based design of a series of cyclic hydroxyethylamine BACE1 inhibitors allowed the rational incorporation of prime- and nonprime-side fragments to a central core template without any amide functionality. The core scaffold selection and the structure-activity relationship development were supported by molecular modeling studies and by X-ray analysis of BACE1 complexes with various ligands to expedite the optimization of the series. The direct extension from P1-aryl- and heteroaryl moieties into the S3 binding pocket allowed the enhancement of potency and selectivity over cathepsin D. Restraining the design and synthesis of compounds to a physicochemical property space consistent with central nervous system drugs led to inhibitors with improved blood-brain barrier permeability. Guided by structure-based optimization, we were able to obtain highly potent compounds such as 60p with enzymatic and cellular IC(50) values of 2 and 50 nM, respectively, and with >200-fold selectivity over cathepsin D. Pharmacodynamic studies in APP51/16 transgenic mice at oral doses of 180 μmol/kg demonstrated significant reduction of brain Aβ levels.

    Related Citations: 
    • Structure-Based Design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors
      Rueeger, H., Rondeau, J.M., McCarthy, C., Moebitz, H., Tintelnot-Blomley, M., Neumann, U., Desrayaud, S.
      (2011) Bioorg Med Chem Lett 21: 1942
    Organizational Affiliation: 

    Department of Global Discovery Chemistry, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland. heinrich.rueeger@novartis.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C402Homo sapiensMutation(s): 0 
Gene Names: BACE, BACE1, 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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BXD
Query on BXD
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
G [auth C]		(3S,4S,5R)-3-(4-amino-3-{[(2R)-3-ethoxy-1,1,1-trifluoropropan-2-yl]oxy}-5-fluorobenzyl)-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1,1-dioxide
C28 H38 F4 N2 O5 S
UJZFSYZNJMWXJO-NJONLQHESA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth B],
H [auth C]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BXD BindingDB:  4D8C IC50: min: 2, max: 126 (nM) from 2 assay(s)
Binding MOAD:  4D8C IC50: 2 (nM) from 1 assay(s)
PDBBind:  4D8C IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.133α = 90
b = 103.505β = 103.98
c = 100.409γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
CNXphasing
CNXrefinement

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: 2012-11-21
    Type: Initial release