5WKM

2.25 A resolution structure of MERS 3CL protease in complex with piperidine-based peptidomimetic inhibitor 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element.

Galasiti Kankanamalage, A.C.Kim, Y.Damalanka, V.C.Rathnayake, A.D.Fehr, A.R.Mehzabeen, N.Battaile, K.P.Lovell, S.Lushington, G.H.Perlman, S.Chang, K.O.Groutas, W.C.

(2018) Eur J Med Chem 150: 334-346

  • DOI: 10.1016/j.ejmech.2018.03.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • There are currently no approved vaccines or small molecule therapeutics available for the prophylaxis or treatment of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infections. MERS-CoV 3CL protease is essential for viral replication; conseq ...

    There are currently no approved vaccines or small molecule therapeutics available for the prophylaxis or treatment of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infections. MERS-CoV 3CL protease is essential for viral replication; consequently, it is an attractive target that provides a potentially effective means of developing small molecule therapeutics for combatting MERS-CoV. We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The mechanism of action of the compounds and the structural determinants associated with binding were illuminated using X-ray crystallography.


    Organizational Affiliation

    Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orf1a protein
A
313Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)Mutation(s): 0 
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Go to UniProtKB:  K9N638
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N02
Query on N02

Download SDF File 
Download CCD File 
A
(1S,2S)-2-{[N-({[1-(tert-butoxycarbonyl)-4-ethylpiperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
bound form
C26 H46 N4 O10 S
XQPCHNVZRFSEQT-OZIGNCPNSA-N
 Ligand Interaction
B6Y
Query on B6Y

Download SDF File 
Download CCD File 
A
(1R,2S)-2-{[N-({[1-(tert-butoxycarbonyl)-4-ethylpiperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
bound form
C26 H46 N4 O10 S
XQPCHNVZRFSEQT-ZVVDCOBXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.626α = 90.00
b = 58.114β = 112.07
c = 49.862γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP30GM110761

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release