7K0F | pdb_00007k0f

1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with a deuterated GC376 alpha-ketoamide analog (compound 5)

• PDB DOI: https://doi.org/10.2210/pdb7K0F/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-09-04 Released: 2021-01-13 
• Deposition Author(s): Lovell, S., Kashipathy, M.M., Battaile, K.P., Chamandi, S.D., Nguyen, H.N., Kim, Y., Chang, K.O., Groutas, W.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Postinfection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection.

Dampalla, C.S., Zheng, J., Perera, K.D., Wong, L.R., Meyerholz, D.K., Nguyen, H.N., Kashipathy, M.M., Battaile, K.P., Lovell, S., Kim, Y., Perlman, S., Groutas, W.C., Chang, K.O.

(2021) Proc Natl Acad Sci U S A 118

• PubMed: 34210738 
• DOI: https://doi.org/10.1073/pnas.2101555118
• Primary Citation Related Structures: 
  7K0E, 7K0F, 7K0G, 7K0H


• PubMed Abstract: 
  

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to be a serious global public health threat. The 3C-like protease (3CLpro) is a virus protease encoded by SARS-CoV-2, which is essential for virus replication. We have previously reported a series of small-molecule 3CLpro inhibitors effective for inhibiting replication of human coronaviruses including SARS-CoV-2 in cell culture and in animal models. Here we generated a series of deuterated variants of a 3CLpro inhibitor, GC376, and evaluated the antiviral effect against SARS-CoV-2. The deuterated GC376 displayed potent inhibitory activity against SARS-CoV-2 in the enzyme- and the cell-based assays. The K18-hACE2 mice develop mild to lethal infection commensurate with SARS-CoV-2 challenge doses and were proposed as a model for efficacy testing of antiviral agents. We treated lethally infected mice with a deuterated derivative of GC376. Treatment of K18-hACE2 mice at 24 h postinfection with a derivative (compound 2) resulted in increased survival of mice compared to vehicle-treated mice. Lung virus titers were decreased, and histopathological changes were ameliorated in compound 2-treated mice compared to vehicle-treated mice. Structural investigation using high-resolution crystallography illuminated binding interactions of 3CLpro of SARS-CoV-2 and SARS-CoV with deuterated variants of GC376. Taken together, deuterated GC376 variants have excellent potential as antiviral agents against SARS-CoV-2.

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Organizational Affiliation: 
• Department of Chemistry, Wichita State University, Wichita, KS 67260.
Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242.
Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506.
Department of Pathology, The University of Iowa, Iowa City, IA 52242.
Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047.
NYX, New York Structural Biology Center, Upton, NY 11973.
Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506; [e-mail] [e-mail] [e-mail] [e-mail].
Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242; [e-mail] [e-mail] [e-mail] [e-mail].
Department of Chemistry, Wichita State University, Wichita, KS 67260; [e-mail] [e-mail] [e-mail] [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: 69.41 kDa 
• Atom Count: 4,921 
• Modeled Residue Count: 596 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	309	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VR4 (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy)carbonyl]-L-leucinamide C29 H38 N4 O6 MPMTWRHFCLPCDF-OJJQZRKESA-N
PG4	E [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.246	α = 90
b = 98.532	β = 108
c = 58.962	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Lovell, S., Kashipathy, M.M., Battaile, K.P., Chamandi, S.D., Nguyen, H.N., Kim, Y., Chang, K.O., Groutas, W.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI109039

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2021-07-14
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary