3OVX

Cathepsin S in complex with a covalent inhibitor with an aldehyde warhead


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 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 S
A, B
218Homo sapiensMutation(s): 0 
Gene Names: CTSS
EC: 3.4.22.27
Find proteins for P25774 (Homo sapiens)
Go to Gene View: CTSS
Go to UniProtKB:  P25774
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
O64
Query on O64

Download SDF File 
Download CCD File 
A, B
2-chloro-N-[(1S)-1-formylpropyl]-3-(trifluoromethyl)benzamide
C12 H11 Cl F3 N O2
NPWUKONGKBALPD-ZETCQYMHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
O64IC50: 31 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 85.545α = 90.00
b = 85.545β = 90.00
c = 150.571γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
CrystalCleardata collection
MOLREPphasing
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