Cathepsin K covalently bound to a cyano-pyrimidine inhibitor with improved selectivity over hERG

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

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This is version 1.2 of the entry. See complete history


Optimisation of 2-cyano-pyrimidine inhibitors of cathepsin K: improving selectivity over hERG.

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

(2010) Bioorg Med Chem Lett 20: 6237-6241

  • DOI: https://doi.org/10.1016/j.bmcl.2010.08.101
  • Primary Citation of Related Structures:  
    3O0U, 3O1G

  • PubMed Abstract: 

    Several structure-guided optimisation strategies were explored in order to improve the hERG selectivity profile of cathepsin K inhibitor 1, whilst maintaining its otherwise excellent in vitro and in vivo profile. Ultimately, attenuation of clogP and pK(a) properties proved a successful approach and led to the discovery of a potent analogue 23, which, in addition to the desired selectivity over hERG (>1000-fold), displayed a highly attractive overall profile.

  • Organizational Affiliation

    Merck Research Laboratories, MSD, Newhouse, Lanarkshire, ML1 5SH Scotland, United Kingdom. zoran.rankovic@merck.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
PHAROS:  P43235
GTEx:  ENSG00000143387 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on O47

Download Ideal Coordinates CCD File 
B [auth A]3-{2-[(E)-iminomethyl]-6-propylpyrimidin-4-yl}-N,N-dimethyl-5-(trifluoromethyl)benzamide
C18 H19 F3 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
O47 PDBBind:  3O0U IC50: 12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.695α = 90
b = 48.967β = 90
c = 103.958γ = 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: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description