3KWZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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% ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin KA215Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KWZ
Query on KWZ

Download Ideal Coordinates CCD File 
H [auth A]4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile
C20 H21 F3 N4
XGXDWBUGQKHTSH-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
KWZ PDBBind:  3KWZ IC50: 4 (nM) from 1 assay(s)
BindingDB:  3KWZ IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.814α = 90
b = 55.814β = 90
c = 129.115γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

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: 2014-02-12
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description