3BC3

Exploring inhibitor binding at the S subsites of cathepsin L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Exploring inhibitor binding at the S' subsites of cathepsin L

Chowdhury, S.F.Joseph, L.Kumar, S.Tulsidas, S.R.Bhat, S.Ziomek, E.Menard, R.Sivaraman, J.Purisima, E.O.

(2008) J.Med.Chem. 51: 1361-1368

  • DOI: 10.1021/jm701190v

  • PubMed Abstract: 
  • We report a series of noncovalent, reversible inhibitors of cathepsin L that have been designed to explore additional binding interactions with the S' subsites. The design was based on our previously reported crystal structure that suggested the poss ...

    We report a series of noncovalent, reversible inhibitors of cathepsin L that have been designed to explore additional binding interactions with the S' subsites. The design was based on our previously reported crystal structure that suggested the possibility of engineering increased interactions with the S' subsites ( Chowdhury et al. J. Med. Chem. 2002, 45, 5321-5329 ). A representative of these new inhibitors has been co-crystallized with mature cathepsin L, and the structure has been solved and refined at 2.2 A. The inhibitors described in this work extend farther into the S' subsites of cathepsins than any inhibitors reported in the literature thus far. These interactions appear to make use of a S3' subsite that can potentially be exploited for enhanced specificity and/or affinity.


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin L heavy and light chains
A, B
220Homo 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
OPT
Query on OPT

Download SDF File 
Download CCD File 
A, B
S-benzyl-N-(biphenyl-4-ylacetyl)-L-cysteinyl-N~5~-(diaminomethyl)-D-ornithyl-N-(2-phenylethyl)-L-tyrosinamide
C47 H55 N7 O5 S
IMZNRHOMBTZKJS-IWSHAHEXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OPTKi: 155 nM BINDINGMOAD
OPTKi: 155 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.765α = 90.00
b = 90.929β = 90.00
c = 126.026γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MOLREPphasing
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2017-10-25
    Type: Refinement description