9GLV | pdb_00009glv

Crystal structure of SARS-CoV-2 Mpro with AB-343.

PDB DOI: https://doi.org/10.2210/pdb9GLV/pdb

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

Deposited: 2024-08-28 Released: 2024-12-04
Deposition Author(s): Prasad, A., Blaesse, M., Maskos, K., Steinbacher, S., Konz Makino, D.L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.238 (Depositor), 0.243 (DCC)
R-Value Work:
0.198 (Depositor), 0.206 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biological characterization of AB-343, a novel and potent SARS-CoV-2 M pro inhibitor with pan-coronavirus activity.

McGovern-Gooch, K.R., Mani, N., Gotchev, D., Ardzinski, A., Kowalski, R., Sheraz, M., Micolochick Steuer, H.M., Tercero, B., Wang, X., Wasserman, A., Chen, C.Y., von Konig, K., Maskos, K., Prasad, A., Blaesse, M., Bergmann, A., Konz Makino, D.L., Fan, K.Y., Kultgen, S.G., Lindstrom, A., Nguyen, D., Vega, M., Wang, X., Bracci, N., Weiss, S.R., Cole, A.G., Lam, A.M., Cuconati, A., Sofia, M.J.

(2024) Antiviral Res 232: 106038-106038

PubMed: 39577571 Search on PubMed
DOI: https://doi.org/10.1016/j.antiviral.2024.106038
Primary Citation of Related Structures:
9GLV

PubMed Abstract:
Since the SARS-CoV-2 outbreak, there have been ongoing efforts to identify antiviral molecules with broad coronavirus activity to combat COVID-19. SARS-CoV-2's main protease (M ^pro) is responsible for processing the viral polypeptide into non-structural proteins essential for replication. Here, we present the biological characterization of AB-343, a covalent small-molecule inhibitor of SARS-CoV-2 M ^pro with potent activity in both cell-based (EC ₅₀ = 0.018 μM) and enzymatic (K _i = 0.0028 μM) assays. AB-343 also demonstrated excellent inhibition of M ^pro of other human coronaviruses, including those from the alpha (229E and NL63) and beta (SARS-CoV, MERS, OC43, and HKU1) families, suggesting the compound could be active against future coronaviruses. No change in AB-343 potency was observed against M ^pro of SARS-CoV-2 variants of concern, including Omicron, suggesting that AB-343 could be developed as a treatment against currently circulating coronaviruses. AB-343 also remained active against several M ^pro variants which confer significant resistance to nirmatrelvir and ensitrelvir, which are presently the only M ^pro inhibitors authorized for the treatment of COVID-19, further supporting the evaluation of AB-343 as a novel and potent therapeutic for COVID-19 and other coronaviruses.

Organizational Affiliation

Arbutus Biopharma, Inc., Warminster, PA, USA. Electronic address: kmcgoverngooch@gmail.com.

Macromolecule Content

Total Structure Weight: 69.18 kDa
Atom Count: 5,184
Modeled Residue Count: 605
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 EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IMY (Subject of Investigation/LOI) Query on A1IMY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	(1S,3S,4S)-N-[(2S)-1-azanylidene-3-[(3S)-5,5-dimethyl-2-oxidanylidene-pyrrolidin-3-yl]propan-2-yl]-2-[(2R)-3-cyclobutyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]propanoyl]-5,5-bis(fluoranyl)-2-azabicyclo[2.2.2]octane-3-carboxamide C₂₆ H₃₆ F₅ N₅ O₄ KLQWCIBSZOJHLB-VIUKOLAESA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]