4D89 Crystal Structure of Human Beta Secretase in Complex with NVP-BXD552, derived from a soaking experiment date 2012-01-10
authors Rondeau, J.M., Bourgier, E.
compound source
symmetry
R_factor
R_Free 0.2110
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.65
ligand BXD BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDiscovery 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 JM, Mobitz H, Machauer R, Jacobson L, Staufenbiel M, Desrayaud S, Neumann U, J Med Chem. 2012 Apr 12;55(7):3364-86. Epub 2012 Mar 21. PMID:22380629
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (4d89.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 4D89
  • CSU: Contacts of Structural Units for 4D89
  • Structure Factors (399 Kb)
  • Retrieve 4D89 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D89 from S2C, [Save to disk]
  • Re-refined 4d89 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4D89 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 4D89
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4D89, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d89] [4d89_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4D89
  • Community annotation for 4D89 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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