4D85

Crystal Structure of Human Beta Secretase in Complex with NVP-BVI151


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report



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:  
    4D8C, 4D88, 4D89, 4D83, 4D85, 3VF3, 3VEU, 3VG1

  • 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 s ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A408Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0GU
Query on 0GU

Download CCD File 
A
(3R,4S,5S)-3-[(3-tert-butylbenzyl)amino]-5-[(4,4,7'-trifluoro-1',2'-dihydrospiro[cyclohexane-1,3'-indol]-5'-yl)methyl]tetrahydro-2H-thiopyran-4-ol 1,1-dioxide
C30 H39 F3 N2 O3 S
YSVPVGYQIWTLEZ-UDZXTKBFSA-N
 Ligand Interaction
IOD
Query on IOD

Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0GUIC50 :  140   nM  PDBBind
0GUIC50:  3530   nM  BindingDB
0GUIC50:  140   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.656α = 90
b = 102.656β = 90
c = 170.902γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-21
    Type: Initial release