3H8C

A combined crystallographic and molecular dynamics study of cathepsin-L retro-binding inhibitors (compound 14)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Combined Crystallographic and Molecular Dynamics Study of Cathepsin L Retrobinding Inhibitors

Shenoy, R.T.Chowdhury, S.F.Kumar, S.Joseph, L.Purisima, E.O.Sivaraman, J.

(2009) J.Med.Chem. --: --

  • DOI: 10.1021/jm900596y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the crystal structures of three noncovalent retrobinding inhibitors in complex with mature cathepsin L up to resolutions of 2.5, 1.8, and 2.5 A, respectively. These inhibitors were Bpa-(Nepsilon-Bpa)Lys-DArg-Tyr-Npe, Bpa-(Nepsilon-Bpa)Lys-D ...

    We report the crystal structures of three noncovalent retrobinding inhibitors in complex with mature cathepsin L up to resolutions of 2.5, 1.8, and 2.5 A, respectively. These inhibitors were Bpa-(Nepsilon-Bpa)Lys-DArg-Tyr-Npe, Bpa-(Nepsilon-Bpa)Lys-DArg-Phe-Npe, and Bpa-MCys-DArg-Phe-Npe, where Bpa = biphenylacetyl and Pea = N-phenylethyl. These were selected to clarify the binding mode of the biphenyl groups in the S' subsites because the addition of a second biphenyl does not improve potency. Examination of the symmetry-related monomers in the crystal structures revealed inhibitor-inhibitor crystal packing interactions. Molecular dynamics simulations were then used to explore the structure and dynamical behavior of the isolated protein-ligand complexes in solution. In the simulations, the backbone biphenyl groups for all three inhibitors ended up in the same location despite having started out in different orientations in the initial crystal structure conformations. The lack of improved potency of the larger inhibitors over the smaller one is attributed to a correspondingly greater entropic cost of binding.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin L1
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
NSZ
Query on NSZ

Download SDF File 
Download CCD File 
A, B
N-(biphenyl-4-ylacetyl)-S-methyl-L-cysteinyl-D-arginyl-N-(2-phenylethyl)-L-phenylalaninamide
C41 H49 N7 O4 S
UYRQVAFRIYOHSH-SBPNQFBHSA-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 %)
NSZKi: 19 nM BINDINGMOAD
NSZKi: 19 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.922α = 90.00
b = 59.011β = 90.00
c = 132.616γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
d*TREKdata reduction
CNSrefinement
AMoREphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-11-12
    Type: Other