3BC3

Exploring inhibitor binding at the S subsites of cathepsin L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 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
  • Primary Citation of Related Structures:  
    3BC3

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin L heavy and light chainsAB220Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OPT
Query on OPT

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,BL-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OPTKi:  155   nM  Binding MOAD
OPTKi :  155   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 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
b = 90.929β = 90
c = 126.026γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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