8F02 | pdb_00008f02

SARS-CoV-2 Main Protease (Mpro) in Complex with ML2006a4

• PDB DOI: https://doi.org/10.2210/pdb8F02/pdb

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


• Deposited: 2022-11-01 Released: 2023-10-11 
• Deposition Author(s): Westberg, M., Fernandez, D., Lin, M.Z.
• Funding Organization(s): Novo Nordisk Foundation, Other private, 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: 2.00 Å
• R-Value Free: 
  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations.

Westberg, M., Su, Y., Zou, X., Huang, P., Rustagi, A., Garhyan, J., Patel, P.B., Fernandez, D., Wu, Y., Hao, C., Lo, C.W., Karim, M., Ning, L., Beck, A., Saenkham-Huntsinger, P., Tat, V., Drelich, A., Peng, B.H., Einav, S., Tseng, C.K., Blish, C., Lin, M.Z.

(2024) Sci Transl Med 16: eadi0979-eadi0979

• PubMed: 38478629 
• DOI: https://doi.org/10.1126/scitranslmed.adi0979
• Primary Citation Related Structures: 
  7SET, 7SF1, 7SF3, 7U92, 7UUG, 7UUP, 8EZV, 8EZZ, 8F02, 8F2C, 8F2D


• PubMed Abstract: 
  

  Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M ^pro ) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 M ^pro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.

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Organizational Affiliation: 
• Department of Neurobiology, Stanford University, Stanford, CA 94305, USA.
Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark.
Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark.
Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China.
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
Department of Medicine, Stanford University, Stanford, CA 94305, USA.
Stanford In Vitro Biosafety Level 3 Service Center, Stanford University, Stanford, CA 94305, USA.
Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA.
Sarafan ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA 94305, USA.
Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA.
Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.

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)

Macromolecule Content 

• Total Structure Weight: 34.46 kDa 
• Atom Count: 2,477 
• Modeled Residue Count: 306 
• 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): 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X6T (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-N-{(2S,3R)-4-(3,3-dimethylazetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C30 H46 F3 N5 O6 KOJLJTKYOSKMNV-YTNBPZCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.649	α = 90
b = 63.231	β = 90
c = 103.798	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Westberg, M., Fernandez, D., Lin, M.Z.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF18OC0031816
Other private		--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171421

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Structure summary
• Version 1.3: 2026-03-04
  Changes: Refinement description