3OVZ

Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Trifluoromethylphenyl as P2 for ketoamide-based cathepsin S inhibitors.

Cai, J.Robinson, J.Belshaw, S.Everett, K.Fradera, X.van Zeeland, M.van Berkom, L.van Rijnsbergen, P.Popplestone, L.Baugh, M.Dempster, M.Bruin, J.Hamilton, W.Kinghorn, E.Westwood, P.Kerr, J.Rankovic, Z.Arbuckle, W.Bennett, D.J.Jones, P.S.Long, C.Martin, I.Uitdehaag, J.C.Meulemans, T.

(2010) Bioorg Med Chem Lett 20: 6890-6894

  • DOI: 10.1016/j.bmcl.2010.10.012
  • Primary Citation of Related Structures:  
    3OVX, 3OVZ

  • PubMed Abstract: 
  • The trifluoromethylphenyl P2 motif from previously reported heteroarylnitrile series has been successfully applied for the design and synthesis of highly potent novel ketoamide-based cathepsin S inhibitors. The key in this process is the change of th ...

    The trifluoromethylphenyl P2 motif from previously reported heteroarylnitrile series has been successfully applied for the design and synthesis of highly potent novel ketoamide-based cathepsin S inhibitors. The key in this process is the change of the torsion angle between the P2 phenyl ring and the attached secondary amide by adding a small Cl, F, or Me group at the 2-position.


    Organizational Affiliation

    Merck Research Laboratories, MSD, Newhouse, Lanarkshire, United Kingdom. jiaqiang.cai@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin KA213Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Explore P43235 
Go to UniProtKB:  P43235
NIH Common Fund Data Resources
PHAROS  P43235
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O96
Query on O96

Download CCD File 
A
N-[(1S)-3-amino-1-ethyl-2,3-dioxopropyl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide
C19 H17 Cl F3 N3 O4
VMSZYKRQEOLBRN-LBPRGKRZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
O96IC50:  8.699999809265137   nM  BindingDB
O96IC50 :  8.699999809265137   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.741α = 90
b = 55.741β = 90
c = 128.916γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-12
    Changes: Derived calculations
  • Version 1.3: 2012-05-09
    Changes: Data collection
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation