2AUX

Cathepsin K complexed with a semicarbazone inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb2AUX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-08-29 Released: 2006-08-08 
• Deposition Author(s): 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., Shewchuk, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.253 
• R-Value Work: 0.198 

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

• PubMed: 16290936 
• DOI: https://doi.org/10.1016/j.bmcl.2005.10.108
• Primary Citation of 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.

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Organizational Affiliation: 

Department of Research Bioanalysis and Drug Metabolism, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.83 kDa 
• Atom Count: 1,748 
• Modelled Residue Count: 213 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	215	Homo sapiens	Mutation(s): 0  Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens) Explore P43235  Go to UniProtKB:  P43235
PHAROS:  P43235

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CT1	B [auth A]	(1R)-2-METHYL-1-(PHENYLMETHYL)PROPYL[(1S)-1-FORMYLPENTYL]CARBAMATE C18 H27 N O3 ZLZXUNHJWVLGTE-DLBZAZTESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CT1	PDBBind:  2AUX	IC50: 0.5 (nM) from 1 assay(s)
	BindingDB:  2AUX	IC50: 0.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.253 
• R-Value Work: 0.198 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.39	α = 90
b = 61.39	β = 90
c = 110.15	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): 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., Shewchuk, L.M.

Revision History  

• 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