3H8B

A combined crystallographic and molecular dynamics study of cathepsin-L retro-binding inhibitors(compound 9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 

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 52: 6335-6346

  • DOI: 10.1021/jm900596y
  • Primary Citation of Related Structures:  
    3H8B, 3H89, 3H8C

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin L1A, B, C, D, E, F220Homo sapiensMutation(s): 0 
Gene Names: Cathepsin LCTSLCTSL1
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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NSY
Query on NSY

Download CCD File 
A, B, C, D, E, F
N~2~,N~6~-bis(biphenyl-4-ylacetyl)-L-lysyl-D-arginyl-N-(2-phenylethyl)-L-phenylalaninamide
C57 H64 N8 O5
YLNSEFZQVOPLSQ-HLRAQNEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NSYKi:  510.9999694824219   nM  Binding MOAD
NSYKi :  510.9999694824219   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.99α = 90
b = 99.234β = 90.05
c = 206.462γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Database references