Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.96 kDa 
• Atom Count: 1695 
• Modelled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

5T6U

Crystal structure of mouse cathepsin K at 2.9 Angstroms resolution.

• PDB DOI: 10.2210/pdb5T6U/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2016-09-01 Released: 2017-01-18 
• Deposition Author(s): Law, S., Aguda, A., Nguyen, N., Brayer, G., Bromme, D.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

Literature

Identification of mouse cathepsin K structural elements that regulate the potency of odanacatib.

Law, S., Andrault, P.M., Aguda, A.H., Nguyen, N.T., Kruglyak, N., Brayer, G.D., Bromme, D.

(2017) Biochem J 474: 851-864

• PubMed: 28049758 
• DOI: 10.1042/BCJ20160985
• Primary Citation of Related Structures:  
  5T6U, 5TDI, 5TUN


• PubMed Abstract: 
  

Cathepsin K (CatK) is the predominant mammalian bone-degrading protease and thus an ideal target for antiosteoporotic drug development. Rodent models of osteoporosis are preferred due to their close reflection of the human disease and their ease of handling, genetic manipulation and economic affordability. However, large differences in the potency of CatK inhibitors for the mouse/rat vs. the human protease orthologs have made it impossible to use rodent models. This is even more of a problem considering that the most advanced CatK inhibitors, including odanacatib (ODN) and balicatib, failed in human clinical trials due to side effects and rodent models are not available to investigate the mechanism of these failures. Here, we elucidated the structural elements of the potency differences between mouse and human CatK (hCatK) using ODN. We determined and compared the structures of inhibitor-free mouse CatK (mCatK), hCatK and ODN bound to hCatK. Two structural differences were identified and investigated by mutational analysis. Humanizing subsite 2 in mCatK led to a 5-fold improvement of ODN binding, whereas the replacement of Tyr61 in mCatK with Asp resulted in an hCatK with comparable ODN potency. Combining both sites further improved the inhibition of the mCatK variant. Similar results were obtained for balicatib. These findings will allow the generation of transgenic CatK mice that will facilitate the evaluation of CatK inhibitor adverse effects and to explore routes to avoid them.

---

Organizational Affiliation: 

Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z3.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	215	Mus musculus	Mutation(s): 0  Gene Names: Ctsk EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P55097 (Mus musculus) Explore P55097  Go to UniProtKB:  P55097
IMPC:  MGI:107823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.92	α = 90
b = 43.26	β = 90
c = 133.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-01 
• Released Date: 2017-01-18 
Deposition Author(s): Law, S., Aguda, A., Nguyen, N., Brayer, G., Bromme, D.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP89974
Canadian Institutes of Health Research (CIHR)	Canada	MOP201209

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Data collection
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary