9GV2 | pdb_00009gv2

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor FP237 (compound 8p in publication)

PDB DOI: https://doi.org/10.2210/pdb9GV2/pdb

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

Deposited: 2024-09-20 Released: 2025-01-29
Deposition Author(s): Strater, N., Sylvester, K., Muller, C.E., Flury, P., Kruger, N., Breidenbach, J., Guetschow, M., Laufer, S.A., Pillaiyar, T.
Funding Organization(s): Volkswagen Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.281 (Depositor), 0.281 (DCC)
R-Value Work:
0.223 (Depositor), 0.227 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Design, Synthesis, and Unprecedented Interactions of Covalent Dipeptide-Based Inhibitors of SARS-CoV-2 Main Protease and Its Variants Displaying Potent Antiviral Activity.

Flury, P., Kruger, N., Sylvester, K., Breidenbach, J., Al Hamwi, G., Qiao, J., Chen, Y., Rocha, C., Serafim, M.S.M., Barbosa da Silva, E., Pohlmann, S., Poso, A., Kronenberger, T., Rox, K., O'Donoghue, A.J., Yang, S., Strater, N., Gutschow, M., Laufer, S.A., Muller, C.E., Pillaiyar, T.

(2025) J Med Chem 68: 3626-3652

PubMed: 39813204 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c02254
Primary Citation of Related Structures:
9GV2

PubMed Abstract:
The main protease (M ^pro) of SARS-CoV-2 is a key drug target for the development of antiviral therapeutics. Here, we designed and synthesized a series of small-molecule peptidomimetics with various cysteine-reactive electrophiles. Several compounds were identified as potent SARS-CoV-2 M ^pro inhibitors, including compounds 8n (IC ₅₀ = 0.0752 μM), 8p (IC ₅₀ = 0.0887 μM), 8r (IC ₅₀ = 0.0199 μM), 10a (IC ₅₀ = 0.0376 μM), 10c (IC ₅₀ = 0.0177 μM), and 10f (IC ₅₀ = 0.0130 μM). Most of them additionally inhibited cathepsin L and were also active against SARS-CoV-1 and MERS-CoV M ^pro. In Calu-3 cells, several inhibitors, including 8r , 10a , and 10c , displayed high antiviral activity in the nanomolar range without showing cellular toxicity. The cocrystal structure of SARS-CoV-2 M ^pro in complex with 8p revealed covalent binding to the enzyme's catalytic residue Cys145 and showed specific, unprecedented interactions within the substrate binding pocket. Compounds 10c and especially 8n were effective against a panel of naturally occurring nirmatrelvir-resistant mutants, particularly E166V, and showed metabolic stability and additional favorable pharmacokinetic properties, making it a suitable candidate for further preclinical development.

Organizational Affiliation

Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.

Macromolecule Content

Total Structure Weight: 69.23 kDa
Atom Count: 4,806
Modeled Residue Count: 610
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IPK (Subject of Investigation/LOI) Query on A1IPK Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	(2S)-2-[2-(3-methoxyphenoxy)ethanoylamino]-4-methyl-N-[(2S)-3-oxidanylidene-1-phenyl-pentan-2-yl]pentanamide C₂₆ H₃₄ N₂ O₅ SKKDMKCPTJKHEB-GOTSBHOMSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A]	I [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]