3KWB | pdb_00003kwb

Structure of CatK covalently bound to a dioxo-triazine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3KWB/pdb

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


• Deposited: 2009-12-01 Released: 2010-04-07 
• Deposition Author(s): Uitdehaag, J.C.M., van Zeeland, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.263 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Dioxo-triazines as a novel series of cathepsin K inhibitors

Rankovic, Z., Cai, J., Fradera, X., Dempster, M., Mistry, A., Mitchell, A., Long, C., Hamilton, E., King, A., Boucharens, S., Jamieson, C., Gillespie, J., Cumming, I., Uitdehaag, J., van Zeeland, M.

(2010) Bioorg Med Chem Lett 20: 1488-1490

• PubMed: 20153187 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.116
• Primary Citation of Related Structures:  
  3KWB


• PubMed Abstract: 
  

  A novel dioxo-triazine series of cathepsin K inhibitors was identified from HTS. A rapid exploratory programme led to the discovery of potent and selective cathepsin K inhibitors, typified by compound 24 which displayed IC(50) values of 17nM against catK and >10,000nM in catL, catB and catS assays.

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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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.86 kDa 
• Atom Count: 3,931 
• Modeled Residue Count: 425 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A [auth X], B [auth Y]	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
ORH	C [auth X], D [auth Y]	3,5-dioxo-4-(3-piperidin-1-ylpropyl)-2-[3-(trifluoromethyl)phenyl]-2,3,4,5-tetrahydro-1,2,4-triazine-6-carbonitrile C19 H20 F3 N5 O2 HKAVWQNLXOMWLR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ORH	BindingDB:  3KWB	IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.263 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.452	α = 90
b = 69.338	β = 98.83
c = 90.85	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Uitdehaag, J.C.M., van Zeeland, M.

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary