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

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 

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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: https://doi.org/10.1016/j.ejmech.2018.03.004
  • Primary Citation of Related Structures:  
    5WKJ, 5WKK, 5WKL, 5WKM

  • 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; 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

    LiS Consulting, Lawrence, KS 66046, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orf1a protein313Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: orf1a
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N638 
Go to UniProtKB:  K9N638
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N638
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B6Y

Download Ideal Coordinates CCD File 
C [auth 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
C26 H46 N4 O10 S
Query on N02

Download Ideal Coordinates CCD File 
B [auth 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
C26 H46 N4 O10 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.626α = 90
b = 58.114β = 112.07
c = 49.862γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110761

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description