4OBZ Hydrolase Hydrolase Inhibitor date Jan 08, 2014
title Structure Of Cathepsin D With Inhibitor 2-(3,4-Dimethoxyphen (4-Methylbenzyl)Carbamimidoyl]Acetamide
authors U.Graedler, P.Czodrowski, C.Tsaklakidis, M.Klein, K.Maskos, B.Leu
compound source
Molecule: Cathepsin D Light Chain
Chain: A, C
Ec: 3.4.23.5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cpsd, Ctsd
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Cathepsin D Heavy Chain
Chain: B, D
Ec: 3.4.23.5
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cpsd, Ctsd
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
230.340 42.454 73.216 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 2S4, NAG enzyme Hydrolase E.C.3.4.23.5 BRENDA
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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4OBZ, from MSDmotif at EBI
  • Fold representative 4obz from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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