4OD9 Structure of Cathepsin D with inhibitor N-(3,4-dimethoxybenzyl)-Nalpha-{N-[(3,4-dimethoxyphenyl)acetyl]carbamimidoyl}-D-phenylalaninamide date
authors Graedler, U., Czodrowski, P., Tsaklakidis, C., Klein, M., Maskos, K., Leuthner, B.
compound source
symmetry
R_factor
R_Free 0.2165
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.90
ligand 2RZ, ACT, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure-based optimization of non-peptidic Cathepsin D inhibitors., Gradler U, Czodrowski P, Tsaklakidis C, Klein M, Werkmann D, Lindemann S, Maskos K, Leuthner B, Bioorg Med Chem Lett. 2014 Jul 25. pii: S0960-894X(14)00778-1. doi:, 10.1016/j.bmcl.2014.07.054. PMID:25086681
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (229 Kb) [Save to disk]
  • Biological Unit Coordinates (4od9.pdb1.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 4OD9
  • CSU: Contacts of Structural Units for 4OD9
  • Structure Factors (515 Kb)
  • Retrieve 4OD9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4OD9 from S2C, [Save to disk]
  • Re-refined 4od9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4OD9 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 4OD9
  • 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 4OD9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4od9] [4od9_A] [4od9_D] [4od9_C] [4od9_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4OD9
  • Community annotation for 4OD9 at PDBWiki (http://pdbwiki.org)

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