3KW9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2010.01.100
  • Primary Citation of Related Structures:  

  • 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 selectivit ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin K
A
215Homo sapiensMutation(s): 0 
Gene Names: CTSK (CTSO, CTSO2)
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Go to Gene View: CTSK
Go to UniProtKB:  P43235
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ORG
Query on ORG

Download SDF File 
Download CCD File 
A
4-(cyclohexylamino)-6-piperazin-1-yl-1,3,5-triazine-2-carbonitrile
C14 H21 N7
ZBLLHXCRPWKVCY-UHFFFAOYSA-N
 Ligand Interaction
TFA
Query on TFA

Download SDF File 
Download CCD File 
A
trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ORGIC50: 1 nM (100) BINDINGDB
ORGIC50: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.391α = 90.00
b = 55.391β = 90.00
c = 128.719γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-19
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Refinement description