3OF9

Structural Basis for Irreversible Inhibition of Human Cathepsin L by a Diazomethylketone Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.761 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for reversible and irreversible inhibition of human cathepsin L by their respective dipeptidyl glyoxal and diazomethylketone inhibitors.

Shenoy, R.T.Sivaraman, J.

(2011) J.Struct.Biol. 173: 14-19

  • DOI: 10.1016/j.jsb.2010.09.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cathepsin L plays a key role in many pathophysiological conditions including rheumatoid arthritis, tumor invasion and metastasis, bone resorption and remodeling. Here we report the crystal structures of two analogous dipeptidyl inhibitor complexes wh ...

    Cathepsin L plays a key role in many pathophysiological conditions including rheumatoid arthritis, tumor invasion and metastasis, bone resorption and remodeling. Here we report the crystal structures of two analogous dipeptidyl inhibitor complexes which inhibit human cathepsin L in reversible and irreversible modes, respectively. To-date, there are no crystal structure reports of complexes of proteases with their glyoxal inhibitors or complexes of cathepsin L and their diazomethylketone inhibitors. These two inhibitors - inhibitor 1, an α-keto-β-aldehyde and inhibitor 2, a diazomethylketone, have different groups in the S1 subsite. Inhibitor 1 [Z-Phe-Tyr (OBut)-COCHO], with a K(i) of 0.6nM, is the most potent, reversible, synthetic peptidyl inhibitor of cathepsin L reported to-date. The structure of the inhibitor 1 complex was refined up to 2.2Å resolution. The structure of the complex of the inhibitor 2 [Z-Phe-Tyr (t-Bu)-diazomethylketone], an irreversible inhibitor that can inactivate cathepsin L at μM concentrations, was refined up to 1.76Å resolution. These two inhibitors have substrate-like interactions with the active site cysteine (Cys25). Inhibitor 1 forms a tetrahedral hemithioacetal adduct, whereas the inhibitor 2 forms a thioester with Cys25. The inhibitor 1 β-aldehyde group is shown to make a hydrogen bond with catalytic His163, whereas the ketone carbonyl oxygen of the inhibitor 2 interacts with the oxyanion hole. tert-Butyl groups of both inhibitors are found to make several non-polar contacts with S' subsite residues of cathepsin L. These studies, combined with other complex structures of cathepsin L, reveal the structural basis for their potency and selectivity.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin L1
A
221Homo sapiensMutation(s): 0 
Gene Names: CTSL (CTSL1)
EC: 3.4.22.15
Find proteins for P07711 (Homo sapiens)
Go to Gene View: CTSL
Go to UniProtKB:  P07711
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I0X
Query on I0X

Download SDF File 
Download CCD File 
A
Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-1-(4-tert-butoxybenzyl)-3-diazo-2-oxopropyl]-L-phenylalaninamide
Z-Phe-Tyr(t-Bu)-diazomethylketone
C31 H34 N4 O5
CGONKNHDBTYOOC-SVBPBHIXSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000784 (I0X)
Query on PRD_000784
ANALPHA-[(BENZYLOXY)CARBONYL]-N-[(1S)-1-(4-TERT-BUTOXYBENZYL)-3-DIAZO-2-OXOPROPYL]-L-PHENYLALANINAMIDEPeptide-like / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.761 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 85.557α = 90.00
b = 85.557β = 90.00
c = 50.201γ = 120.00
Software Package:
Software NamePurpose
CBASSdata collection
SCALEPACKdata scaling
HKL-2000data scaling
PHENIXrefinement
CNSrefinement
HKL-2000data reduction
DENZOdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-12-12
    Type: Other
  • Version 1.3: 2017-11-08
    Type: Advisory, Refinement description
  • Version 1.4: 2019-07-17
    Type: Data collection, Derived calculations, Refinement description