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

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report

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
PHAROS:  P43235
GTEx:  ENSG00000143387 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ORG

Download Ideal Coordinates CCD File 
B [auth A]4-(cyclohexylamino)-6-piperazin-1-yl-1,3,5-triazine-2-carbonitrile
C14 H21 N7
Query on TFA

Download Ideal Coordinates CCD File 
C [auth A]trifluoroacetic acid
C2 H F3 O2
Binding Affinity Annotations 
IDSourceBinding 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

  • 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 = 55.391α = 90
b = 55.391β = 90
c = 128.719γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report

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: 2013-06-19
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description