2H7J

Crystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of selective, nonpeptidic nitrile inhibitors of cathepsin s using the substrate activity screening method.

Patterson, A.W.Wood, W.J.Hornsby, M.Lesley, S.Spraggon, G.Ellman, J.A.

(2006) J.Med.Chem. 49: 6298-6307

  • DOI: 10.1021/jm060701s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The substrate activity screening method, a substrate-based fragment identification and optimization method for the development of enzyme inhibitors, was previously applied to cathepsin S to obtain low nanomolar 1,4-disubstituted-1,2,3-triazole-based ...

    The substrate activity screening method, a substrate-based fragment identification and optimization method for the development of enzyme inhibitors, was previously applied to cathepsin S to obtain low nanomolar 1,4-disubstituted-1,2,3-triazole-based aldehyde inhibitors (Wood, W. J. L.; Patterson, A. W.; Tsuruoka, H.; Jain, R. K.; Ellman, J. A. J. Am. Chem. Soc. 2005, 127, 15521-15527). Replacement of the metabolically labile aldehyde pharmacophore with the nitrile pharmacophore provided inhibitors with moderate potency for cathepsin S. The inhibitors showed good selectivity over cathepsins B and L but no selectivity over cathepsin K. X-ray structures of two crystal forms (1.5 and 1.9 A) of a complex between cathepsin S and a triazole inhibitor incorporating a chloromethyl ketone pharmacophore guided the design of triazole substrates with increased cleavage efficiency and selectivity for cathepsin S over cathepsins B, L, and K. Conversion of select substrates to nitrile inhibitors yielded a low molecular weight (414 Da) and potent (15 nM) cathepsin S inhibitor that showed >1000-fold selectivity over cathepsins B, L, and K.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin S
A, B
220Homo 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
P15
Query on P15

Download SDF File 
Download CCD File 
A
2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
C13 H28 O7
FHHGCKHKTAJLOM-UHFFFAOYSA-N
 Ligand Interaction
H7J
Query on H7J

Download SDF File 
Download CCD File 
A, B
N-[(1S)-1-{1-[(1R,3E)-1-ACETYLPENT-3-EN-1-YL]-1H-1,2,3-TRIAZOL-4-YL}-1,2-DIMETHYLPROPYL]BENZAMIDE
C21 H28 N4 O2
OEHUTYXPQSSKAK-RVLLMHTFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.161 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 85.222α = 90.00
b = 85.222β = 90.00
c = 150.754γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance