9MVM | pdb_00009mvm

Crystal Structure of SARS-CoV-2 Main Protease (Mpro)in Complex with Inhibitor AVI-3318

• PDB DOI: https://doi.org/10.2210/pdb9MVM/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-01-15 Released: 2025-07-23 
• Deposition Author(s): Diallo, A., Gumpena, R., Verba, K.
• 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: 1.96 Å
• R-Value Free: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus M Pro inhibitors with potent in vivo efficacy.

Detomasi, T.C., Degotte, G., Huang, S., Suryawanshi, R.K., Diallo, A., Lizzadro, L., Zapatero-Belinchon, F.J., Taha, T.Y., Li, J., Richards, A.L., Hantz, E.R., Alam, Z., Montano, M., McCavitt-Malvido, M., Gumpena, R., Partridge, J.R., Correy, G.J., Matsui, Y., Charvat, A.F., Glenn, I.S., Rosecrans, J., Revalde, J.L., Anderson, D., Hultquist, J.F., Arkin, M.R., Neitz, R.J., Swaney, D.L., Krogan, N.J., Shoichet, B.K., Verba, K.A., Ott, M., Renslo, A.R., Craik, C.S.

(2025) Sci Adv 11: eadt7836-eadt7836

• PubMed: 40267184 
• DOI: https://doi.org/10.1126/sciadv.adt7836
• Primary Citation Related Structures: 
  9MVM, 9MVO, 9MVP, 9MVQ


• PubMed Abstract: 
  

  The main protease (M ^Pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a validated drug target. Starting with a lead-like dihydrouracil chemotype identified in a large-library docking campaign, we improved M ^Pro inhibition >1000-fold by engaging additional M ^Pro subsites and using a latent electrophile to engage Cys ¹⁴⁵ . Advanced leads from this series show pan-coronavirus antiviral activity, low clearance in mice, and for AVI-4773 , a rapid reduction in viral titers >1,000,000 after just three doses. Both compounds are well distributed in mouse tissues, including brain, where concentrations >1000× the 90% effective concentration are observed 8 hours after oral dosing for AVI-4773 . AVI-4516 shows minimal inhibition of major cytochrome P450s and human proteases. AVI-4516 also exhibits synergy with the RNA-dependent RNA polymerase inhibitor, molnupiravir, in cellular infection models. Related analogs strongly inhibit nirmatrelvir-resistant M ^Pro mutant virus. The properties of this chemotype are differentiated from existing clinical and preclinical M ^Pro inhibitors and will advance therapeutic development against emerging SARS-CoV-2 variants and other coronaviruses.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 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: 34.95 kDa 
• Atom Count: 2,398 
• Modeled Residue Count: 305 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	314	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
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
A1BTM (Subject of Investigation/LOI)	B [auth A]	1-[(4-chlorothiophen-2-yl)methyl]-3-[(2-oxo-1,2-dihydropyridin-3-yl)methyl]-1,3-diazinane-2,4-dione C15 H14 Cl N3 O3 S CFFQNGKRYYJCIS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.735	α = 90
b = 53.829	β = 101.03
c = 45.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Diallo, A., Gumpena, R., Verba, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI171110

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release