4OBZ Structure of Cathepsin D with inhibitor 2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide date
authors Graedler, U., Czodrowski, P., Tsaklakidis, C., Klein, M., Maskos, K., Leuthner, B.
compound source
symmetry
R_factor
R_Free 0.2325
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.90
ligand 2S4, 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] (221 Kb) [Save to disk]
  • Biological Unit Coordinates (4obz.pdb1.gz) 216 Kb
  • LPC: Ligand-Protein Contacts for 4OBZ
  • CSU: Contacts of Structural Units for 4OBZ
  • Structure Factors (417 Kb)
  • Retrieve 4OBZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4OBZ from S2C, [Save to disk]
  • Re-refined 4obz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4OBZ 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 4OBZ
  • 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 4OBZ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4obz_A] [4obz] [4obz_D] [4obz_C] [4obz_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4OBZ
  • Community annotation for 4OBZ at PDBWiki (http://pdbwiki.org)

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