3KX1 | pdb_00003kx1

Cathepsin K in complex with a selective 2-cyano-pyrimidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3KX1/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.306 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: other

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 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: 24.04 kDa 
• Atom Count: 1,892 
• Modeled 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  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
KX1	B [auth A]	4-cycloheptyl-6-(3-piperidin-1-ylpropyl)pyrimidine-2-carbonitrile C20 H30 N4 UTNIKRVBYGTXDR-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
KX1	BindingDB:  3KX1	IC50: 100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.306 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.069	α = 90
b = 56.069	β = 90
c = 128.829	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Fradera, X., 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: 2014-02-12
  Changes: Database references
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary