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 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    3MJ5

  • 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 diverse chemical library ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicase polyprotein 1aA, B316Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1aORF1 (nsp3) residues 1544-1855
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt)
UniProt
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus)
Explore P0C6U8 
Go to UniProtKB:  P0C6U8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GRM (Subject of Investigation/LOI)
Query on GRM

Download Ideal Coordinates CCD File 
C [auth A], E [auth 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GRM PDBBind:  3MJ5 IC50: 320 (nM) from 1 assay(s)
BindingDB:  3MJ5 IC50: min: 320, max: 1200 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.397α = 90
b = 74.129β = 103.02
c = 96.895γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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