8D4K | pdb_00008d4k

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Y Mutant in Complex with Inhibitor GC376

• PDB DOI: https://doi.org/10.2210/pdb8D4K/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-06-02 Released: 2022-07-13 
• Deposition Author(s): Lewandowski, E.M., Hu, Y., Tan, H., Wang, J., Chen, Y.
• 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: 1.89 Å
• R-Value Free: 
  0.224 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.

Hu, Y., Lewandowski, E.M., Tan, H., Zhang, X., Morgan, R.T., Zhang, X., Jacobs, L.M.C., Butler, S.G., Gongora, M.V., Choy, J., Deng, X., Chen, Y., Wang, J.

(2022) bioRxiv 

• PubMed: 36119652 
• DOI: https://doi.org/10.1101/2022.06.28.497978
• Primary Citation Related Structures: 
  8D4J, 8D4K, 8D4L, 8D4M, 8D4N


• PubMed Abstract: 
  

  The SARS-CoV-2 main protease (M ^pro ) is the drug target of Pfizer’s oral drug Paxlovid. The emergence of SARS-CoV-2 variants with mutations in M ^pro raised the alarm of potential drug resistance. In this study, we identified 100 naturally occurring M ^pro mutations located at the nirmatrelvir binding site, among which 20 mutants, including S144M/F/A/G/Y, M165T, E166G, H172Q/F, and Q192T/S/L/A/I/P/H/V/W/C/F, showed comparable enzymatic activity to the wild-type (k _cat /K _m <10-fold change) and resistance to nirmatrelvir (K _i >10-fold increase). X-ray crystal structures were determined for seven representative mutants with and/or without GC-376/nirmatrelvir. Viral growth assay showed that M ^pro mutants with reduced enzymatic activity led to attenuated viral replication. Overall, our study identified several drug resistant hot spots that warrant close monitoring for possible clinical evidence of Paxlovid resistance. Paxlovid resistant SARS-CoV-2 viruses with mutations in the main protease have been identified from clinical isolates.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, NJ, 08854, United States.
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States.
Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, United States.
Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, 74078, United States.
Department Biology, School of Arts and Sciences, the Catholic University of America, Washington DC, 20064, United States.

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: 34.34 kDa 
• Atom Count: 2,659 
• Modeled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K36 (Subject of Investigation/LOI)	B [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

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002495 (K36)	B [auth A]	GC376	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.224 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.549	α = 90
b = 53.111	β = 102.67
c = 45.643	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Lewandowski, E.M., Hu, Y., Tan, H., Wang, J., Chen, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158775

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2022-10-05
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary