5WKK | pdb_00005wkk

1.55 A resolution structure of MERS 3CL protease in complex with inhibitor GC813

• PDB DOI: https://doi.org/10.2210/pdb5WKK/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Middle East respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-07-25 Released: 2018-04-04 
• Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Kankanamalage, A.C.G., Kim, Y., Rathnayake, A.D., Chang, K.O., Groutas, W.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.185 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

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

• PubMed: 29544147 
• DOI: https://doi.org/10.1016/j.ejmech.2018.03.004
• Primary Citation 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.
Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA.
IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA.
LiS Consulting, Lawrence, KS 66046, USA.
Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA. Electronic address: [e-mail].
Department of Chemistry, Wichita State University, Wichita, KS 67260, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.6 kDa 
• Atom Count: 2,634 
• Modeled Residue Count: 301 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orf1a protein	A	313	Middle East respiratory syndrome-related coronavirus	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3G	E [auth A]	(1R,2S)-2-[(N-{[2-(3-chlorophenyl)ethoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C22 H32 Cl N3 O8 S OKWOXOSOFIECOU-QUJKESNLSA-N
AW4	D [auth A]	(1S,2S)-2-[(N-{[2-(3-chlorophenyl)ethoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid C22 H32 Cl N3 O8 S OKWOXOSOFIECOU-DBSRCYSRSA-N
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.185 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.584	α = 90
b = 57.999	β = 112.2
c = 49.731	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Kankanamalage, A.C.G., Kim, Y., Rathnayake, A.D., Chang, K.O., Groutas, W.C.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110761

Revision History  

• 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, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary