3KW9

X-ray structure of Cathepsin K covalently bound to a triazine ligand

• PDB DOI: https://doi.org/10.2210/pdb3KW9/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2009-12-01 Released: 2010-03-02 
• Deposition Author(s): Uitdehaag, J.C.M., van Zeeland, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.259 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 

Literature

Design and optimization of a series of novel 2-cyano-pyrimidines as cathepsin K inhibitors.

Rankovic, Z., Cai, J., Kerr, J., Fradera, X., Robinson, J., Mistry, A., Hamilton, E., McGarry, G., Andrews, F., Caulfield, W., Cumming, I., Dempster, M., Waller, J., Scullion, P., Martin, I., Mitchell, A., Long, C., Baugh, M., Westwood, P., Kinghorn, E., Bruin, J., Hamilton, W., Uitdehaag, J., van Zeeland, M., Potin, D., Saniere, L., Fouquet, A., Chevallier, F., Deronzier, H., Dorleans, C., Nicolai, E.

(2010) Bioorg Med Chem Lett 20: 1524-1527

• PubMed: 20149657 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.100
• Primary Citation of Related Structures:  
  3KW9, 3KWZ, 3KX1


• PubMed Abstract: 
  

  Morphing structural features of HTS-derived chemotypes led to the discovery of novel 2-cyano-pyrimidine inhibitors of cathepsin K with good pharmacokinetic profiles, for example, compound 20 showed high catK potency (IC(50)=4nM), >580-fold selectivity over catL and catB, and oral bioavailability in the rat of 52%.

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Organizational Affiliation: 

Schering-Plough Corporation, Newhouse, Lanarkshire, ML1 5SH Scotland, United Kingdom. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 23.92 kDa 
• Atom Count: 1,771 
• Modelled Residue Count: 215 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ORG	B [auth A]	4-(cyclohexylamino)-6-piperazin-1-yl-1,3,5-triazine-2-carbonitrile C14 H21 N7 ZBLLHXCRPWKVCY-UHFFFAOYSA-N
TFA	C [auth A]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ORG	PDBBind:  3KW9	IC50: 1 (nM) from 1 assay(s)
	BindingDB:  3KW9	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.259 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.391	α = 90
b = 55.391	β = 90
c = 128.719	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Uitdehaag, J.C.M., van Zeeland, M.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-19
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary