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

Experimental Data Snapshot

  • Resolution: 1.51 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.243 

Starting Model: other
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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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

  • 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%.

  • Organizational Affiliation

    Schering-Plough Corporation, Newhouse, Lanarkshire, ML1 5SH Scotland, United Kingdom. zoran.rankovic@spcorp.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin K215Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
GTEx:  ENSG00000143387 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
KX1 PDBBind:  3KX1 IC50: 100 (nM) from 1 assay(s)
BindingDB:  3KX1 IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.51 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.243 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.069α = 90
b = 56.069β = 90
c = 128.829γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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