1MHW

Design of non-covalent inhibitors of human cathepsin L. From the 96-residue proregion to optimized tripeptides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Design of non-covalent inhibitors of human cathepsin L. From the 96-residue proregion to optimized tripeptides

Chowdhury, S.Sivaraman, J.Wang, J.Devanathan, G.Lachance, P.Qi, H.Menard, R.Lefebvre, J.Konishi, Y.Cygler, M.Sulea, T.Purisima, E.O.

(2002) J Med Chem 45: 5321-5329

  • DOI: 10.1021/jm020238t
  • Primary Citation of Related Structures:  
    1MHW

  • PubMed Abstract: 
  • A novel series of noncovalent inhibitors of cathepsin L have been designed to mimic the mode of autoinhibition of procathepsin L. Just like the propeptide, these peptide-based inhibitors have a reverse-binding mode relative to a substrate and span bo ...

    A novel series of noncovalent inhibitors of cathepsin L have been designed to mimic the mode of autoinhibition of procathepsin L. Just like the propeptide, these peptide-based inhibitors have a reverse-binding mode relative to a substrate and span both the S' and S subsites of the enzyme active site. In contrast to previous studies in which even moderate truncation of the full-length propeptide led to rapid reduction in potency, these blocked tripeptide-sized inhibitors maintain nanomolar potency. Moreover, these short peptides show higher selectivity (up to 310-fold) for inhibiting cathepsin L over K versus only 2-fold selectivity of the 96-residue propeptide of cathepsin L. A 1.9 A X-ray crystallographic structure of the complex of cathepsin L with one of the inhibitors confirms the designed reverse-binding mode of the inhibitor as well as its noncovalent nature. Enzymatic analysis also shows the inhibitors to be resistant to hydrolysis at elevated concentrations of the enzyme. The mode of inhibition of these molecules provides a general strategy for inhibiting other cathepsins as well as other proteases.


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin LA, B175Homo sapiensMutation(s): 1 
Gene Names: CTSLCTSL1
EC: 3.4.22.15
Find proteins for P07711 (Homo sapiens)
Explore P07711 
Go to UniProtKB:  P07711
NIH Common Fund Data Resources
PHAROS  P07711
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin LC, D42Homo sapiensMutation(s): 0 
Gene Names: CTSLCTSL1
EC: 3.4.22.15
Find proteins for P07711 (Homo sapiens)
Explore P07711 
Go to UniProtKB:  P07711
NIH Common Fund Data Resources
PHAROS  P07711
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
4-biphenylacetyl-Cys-(D)Arg-Tyr-N-(2-phenylethyl) amideE, F, G, H5N/AMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A,BL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000270
Query on PRD_000270
E, F, G, H4-biphenylacetyl-CYS-(D)ARG-TYR-N-(2-phenylethyl) amidePeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.522α = 90
b = 58.632β = 90
c = 151.445γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2014-11-19
    Changes: Non-polymer description
  • Version 1.5: 2017-10-11
    Changes: Refinement description