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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin S222Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000163131 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BLN
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
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