5WKJ

2.05 A resolution structure of MERS 3CL protease in complex with inhibitor GC376


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: 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

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


Macromolecules
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
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K36
Query on K36

Download Ideal Coordinates CCD File 
E [auth A](1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
C21 H31 N3 O8 S
BSPZFJDYQHDZNR-HTCLRFROSA-N
B1S
Query on B1S

Download Ideal Coordinates CCD File 
D [auth A](1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
C21 H31 N3 O8 S
BSPZFJDYQHDZNR-OGNFBWPZSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.807α = 90
b = 58.292β = 112.25
c = 49.785γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



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: 2020-05-20
    Changes: Structure summary
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description