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⇱ RCSB PDB - 2AUZ: Cathepsin K complexed with a semicarbazone inhibitor

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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 2AUZ | pdb_00002auz

Cathepsin K complexed with a semicarbazone inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.239 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.196 (DCC) 

Starting Model: experimental
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wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 

Literature

Semicarbazone-based inhibitors of cathepsin K, are they prodrugs for aldehyde inhibitors?

Adkison, K.K., Barrett, D.G., Deaton, D.N., Gampe, R.T., Hassell, A.M., Long, S.T., McFadyen, R.B., Miller, A.B., Miller, L.R., Payne, J.A., Shewchuk, L.M., Wells-Knecht, K.J., Willard, D.H., Wright, L.L.

(2006) Bioorg Med Chem Lett 16: 978-983

  • DOI: https://doi.org/10.1016/j.bmcl.2005.10.108
  • Primary Citation Related Structures: 
    2AUX, 2AUZ

  • PubMed Abstract: 

    Starting from potent aldehyde inhibitors with poor drug properties, derivatization to semicarbazones led to the identification of a series of semicarbazone-based cathepsin K inhibitors with greater solubility and better pharmacokinetic profiles than their parent aldehydes. Furthermore, a representative semicarbazone inhibitor attenuated bone resorption in an ex vivo rat calvarial bone resorption model. However, based on enzyme inhibition comparisons at neutral pH, semicarbazone hydrolysis rates, and 13C NMR experiments, these semicarbazones probably function as prodrugs of aldehydes.

    • Organizational Affiliation: 
    • Department of Research Bioanalysis and Drug Metabolism, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.

Macromolecule Content 

  • Total Structure Weight: 24.13 kDa 
  • Atom Count: 1,821 
  • Modeled Residue Count: 215 
  • Deposited Residue Count: 215 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cathepsin K215Homo sapiensMutation(s): 0 
Gene Names: CTSK, CTSO, CTSO2
EC: 3.4.22.38
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UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
PHAROS:  P43235
GTEx:  ENSG00000143387 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.239 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.704α = 90
b = 56.704β = 90
c = 130.375γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-02-14
    Changes: Experimental preparation
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-10-30
    Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.