2BDL Hydrolase date Oct 20, 2005
title Cathepsin K Complexed With A Pyrrolidine Ketoamide-Based Inhibitor
authors L.M.Shewchuk
compound source
Molecule: Cathepsin K
Chain: A
Fragment: Mature Form Of Cathepsin K (Residues 115-329)
Synonym: Cathepsin O, Cathepsin X, Cathepsin O2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ctsk, Ctso, Ctso2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.241
length a length b length c angle alpha angle beta angle gamma
38.060 50.338 105.891 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 4PR enzyme Hydrolase E.C. BRENDA

Primary referenceNovel, potent P2-P3 pyrrolidine derivatives of ketoamide-based cathepsin K inhibitors., Barrett DG, Catalano JG, Deaton DN, Hassell AM, Long ST, Miller AB, Miller LR, Ray JA, Samano V, Shewchuk LM, Wells-Knecht KJ, Willard DH Jr, Wright LL, Bioorg Med Chem Lett. 2006 Mar 15;16(6):1735-9. Epub 2006 Jan 11. PMID:16376075
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (2bdl.pdb1.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 2BDL
  • CSU: Contacts of Structural Units for 2BDL
  • Likely Quarternary Molecular Structure file(s) for 2BDL
  • Structure Factors (183 Kb)
  • Retrieve 2BDL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BDL from S2C, [Save to disk]
  • Re-refined 2bdl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BDL 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 2BDL
  • 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 2BDL, from MSDmotif at EBI
  • Fold representative 2bdl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bdl] [2bdl_A]
  • SWISS-PROT database: [P43235]
  • Domain organization of [CATK_HUMAN] by SWISSPFAM
  • Domain found in 2BDL: [Pept_C1 ] by SMART
  • Other resources with information on 2BDL
  • Community annotation for 2BDL at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science