1YK8

Cathepsin K complexed with a cyanamide-based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1YK8/pdb

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


• Deposited: 2005-01-17 Released: 2005-07-19 
• Deposition Author(s): Barrett, D.G., Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Payne, J.A., Shewchuk, L.M., Willard, D.H., Wright, L.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.219 

Starting Model: experimental

Literature

Acyclic cyanamide-based inhibitors of cathepsin K.

Barrett, D.G., Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Payne, J.A., Shewchuk, L.M., Willard, D.H., Wright, L.L.

(2005) Bioorg Med Chem Lett 15: 3039-3043

• PubMed: 15896958 
• DOI: https://doi.org/10.1016/j.bmcl.2005.04.032
• Primary Citation of Related Structures:  
  1YK8


• PubMed Abstract: 
  

  Conversion of the proline-derived cyanamide lead to an acyclic cyanamide capable of forming an additional hydrogen bond with cathepsin K resulted in a large increase in inhibitory activity. An X-ray structure of a co-crystal of a cyanamide with cathepsin K confirmed the enzyme interaction. Furthermore, a representative acyclic cyanamide inhibitor 6r was able to attenuate bone resorption in the rat calvarial model.

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Organizational Affiliation: 

Department of Medicinal Chemistry, 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: 23.69 kDa 
• Atom Count: 1,659 
• 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 GTEx:  ENSG00000143387

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T2M	B [auth A]	TERT-BUTYL 2-CYANO-2-METHYLHYDRAZINECARBOXYLATE C7 H13 N3 O2 SWELYBAPJHIOQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.219 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.383	α = 90
b = 56.383	β = 90
c = 128.431	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
REFMAC	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-19 
Deposition Author(s): Barrett, D.G., Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Payne, J.A., Shewchuk, L.M., Willard, D.H., Wright, L.L.

Revision History  

• Version 1.0: 2005-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary