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 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin K
A
213Homo 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
O96
Query on O96

Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
O96IC50: 8.7 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 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.741α = 90.00
b = 55.741β = 90.00
c = 128.916γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
d*TREKdata reduction
CrystalCleardata collection
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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