3MJ5

Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-ray Structure and Biological Evaluation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation

Ghosh, A.K.Takayama, J.Rao, K.V.Ratia, K.Chaudhuri, R.Mulhearn, D.C.Lee, H.Nichols, D.B.Baliji, S.Baker, S.C.Johnson, M.E.Mesecar, A.D.

(2010) J.Med.Chem. 53: 4968-4979

  • DOI: 10.1021/jm1004489

  • PubMed Abstract: 
  • The design, synthesis, X-ray crystal structure, molecular modeling, and biological evaluation of a series of new generation SARS-CoV PLpro inhibitors are described. A new lead compound 3 (6577871) was identified via high-throughput screening of a div ...

    The design, synthesis, X-ray crystal structure, molecular modeling, and biological evaluation of a series of new generation SARS-CoV PLpro inhibitors are described. A new lead compound 3 (6577871) was identified via high-throughput screening of a diverse chemical library. Subsequently, we carried out lead optimization and structure-activity studies to provide a series of improved inhibitors that show potent PLpro inhibition and antiviral activity against SARS-CoV infected Vero E6 cells. Interestingly, the (S)-Me inhibitor 15 h (enzyme IC(50) = 0.56 microM; antiviral EC(50) = 9.1 microM) and the corresponding (R)-Me 15 g (IC(50) = 0.32 microM; antiviral EC(50) = 9.1 microM) are the most potent compounds in this series, with nearly equivalent enzymatic inhibition and antiviral activity. A protein-ligand X-ray structure of 15 g-bound SARS-CoV PLpro and a corresponding model of 15 h docked to PLpro provide intriguing molecular insight into the ligand-binding site interactions.


    Organizational Affiliation

    Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA. akghosh@purdue.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicase polyprotein 1a
A, B
316Human SARS coronavirusMutation(s): 0 
Find proteins for P0C6U8 (Human SARS coronavirus)
Go to UniProtKB:  P0C6U8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GRM
Query on GRM

Download SDF File 
Download CCD File 
A, B
N-(1,3-benzodioxol-5-ylmethyl)-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide
C26 H28 N2 O3
IVXBCFLWMPMSAP-GOSISDBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GRMIC50: 980 - 1200 nM (100) BINDINGDB
GRMIC50: 320 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.397α = 90.00
b = 74.129β = 103.02
c = 96.895γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance