4OW0

X-Ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases.

Baez-Santos, Y.M.Barraza, S.J.Wilson, M.W.Agius, M.P.Mielech, A.M.Davis, N.M.Baker, S.C.Larsen, S.D.Mesecar, A.D.

(2014) J Med Chem 57: 2393-2412

  • DOI: 10.1021/jm401712t
  • Primary Citation of Related Structures:  
    4OVZ, 4OW0

  • PubMed Abstract: 
  • Structure-guided design was used to generate a series of noncovalent inhibitors with nanomolar potency against the papain-like protease (PLpro) from the SARS coronavirus (CoV). A number of inhibitors exhibit antiviral activity against SARS-CoV infected Vero E6 cells and broadened specificity toward the homologous PLP2 enzyme from the human coronavirus NL63 ...

    Structure-guided design was used to generate a series of noncovalent inhibitors with nanomolar potency against the papain-like protease (PLpro) from the SARS coronavirus (CoV). A number of inhibitors exhibit antiviral activity against SARS-CoV infected Vero E6 cells and broadened specificity toward the homologous PLP2 enzyme from the human coronavirus NL63. Selectivity and cytotoxicity studies established a more than 100-fold preference for the coronaviral enzyme over homologous human deubiquitinating enzymes (DUBs), and no significant cytotoxicity in Vero E6 and HEK293 cell lines is observed. X-ray structural analyses of inhibitor-bound crystal structures revealed subtle differences between binding modes of the initial benzodioxolane lead (15g) and the most potent analogues 3k and 3j, featuring a monofluoro substitution at para and meta positions of the benzyl ring, respectively. Finally, the less lipophilic bis(amide) 3e and methoxypyridine 5c exhibit significantly improved metabolic stability and are viable candidates for advancing to in vivo studies.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University , 915 W. State Street, West Lafayette, Indiana 47907, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
papain-like proteaseA, B316SARS coronavirus UrbaniMutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 3.4.22 (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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S88
Query on S88

Download Ideal Coordinates CCD File 
D [auth A], I [auth B]N-[(3-fluorophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide
C25 H27 F N2 O
XJTWGMHOQKGBDO-GOSISDBHSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A], G [auth A], J [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], H [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A, BL-PEPTIDE LINKINGC3 H7 N O5 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S88IC50:  150   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.421α = 90
b = 74.388β = 104.11
c = 98.328γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Data collection, Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy