1MS6

Dipeptide Nitrile Inhibitor Bound to Cathepsin S.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design and synthesis of dipeptide nitriles as reversible and potent Cathepsin S inhibitors

Ward, Y.D.Thomson, D.S.Frye, L.L.Cywin, C.L.Morwick, T.Emmanuel, M.J.Zindell, R.McNeil, D.Bekkali, Y.Giradot, M.Hrapchak, M.DeTuri, M.Crane, K.White, D.Pav, S.Wang, Y.Hao, M.H.Grygon, C.A.Labadia, M.E.Freeman, D.M.Davidson, W.Hopkins, J.L.Brown, M.L.Spero, D.M.

(2002) J Med Chem 45: 5471-5482

  • DOI: 10.1021/jm020209i
  • Primary Citation of Related Structures:  
    1MS6

  • PubMed Abstract: 
  • The specificity of the immune response relies on processing of foreign proteins and presentation of antigenic peptides at the cell surface. Inhibition of antigen presentation, and the subsequent activation of T-cells, should, in theory, modulate the immune response ...

    The specificity of the immune response relies on processing of foreign proteins and presentation of antigenic peptides at the cell surface. Inhibition of antigen presentation, and the subsequent activation of T-cells, should, in theory, modulate the immune response. The cysteine protease Cathepsin S performs a fundamental step in antigen presentation and therefore represents an attractive target for inhibition. Herein, we report a series of potent and reversible Cathepsin S inhibitors based on dipeptide nitriles. These inhibitors show nanomolar inhibition of the target enzyme as well as cellular potency in a human B cell line. The first X-ray crystal structure of a reversible inhibitor cocrystallized with Cathepsin S is also reported.


    Organizational Affiliation

    Boehringer Ingelheim Pharmaceuticals, Inc. 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, USA. yward@rdg.boehringer-ingelheim.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin SA222Homo sapiensMutation(s): 0 
Gene Names: CTSS
EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens)
Explore P25774 
Go to UniProtKB:  P25774
PHAROS:  P25774
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLN (Subject of Investigation/LOI)
Query on BLN

Download Ideal Coordinates CCD File 
B [auth A]MORPHOLINE-4-CARBOXYLIC ACID [1S-(2-BENZYLOXY-1R-CYANO-ETHYLCARBAMOYL)-3-METHYL-BUTYL]AMIDE
C21 H30 N4 O4
LXEDKIMJQBOMSU-MOPGFXCFSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BLN PDBBind:  1MS6 Kd: 0.3 (nM) from 1 assay(s)
BindingDB:  1MS6 Kd: 0.3 (nM) from 1 assay(s)
IC50: 19 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.162 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.29α = 90
b = 85.29β = 90
c = 150.07γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report




Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance