9D2K | pdb_00009d2k

SARS-CoV-2 Papain-like Protease (PLpro) complex with covalent inhibitor Jun13567

PDB DOI: https://doi.org/10.2210/pdb9D2K/pdb

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

Deposited: 2024-08-08 Released: 2025-03-26
Deposition Author(s): Ansari, A., Tan, B., Ruiz, F.X., Arnold, E., Wang, J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.209 (Depositor), 0.211 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure-Based Design of Covalent SARS-CoV-2 Papain-like Protease Inhibitors.

Tan, B., Liang, X., Ansari, A., Jadhav, P., Tan, H., Li, K., Ruiz, F.X., Arnold, E., Deng, X., Wang, J.

(2024) J Med Chem 67: 20399-20420

PubMed: 39499574 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c01872
Primary Citation of Related Structures:
9D2K

PubMed Abstract:
The COVID-19 pandemic is caused by SARS-CoV-2, a highly transmissible and pathogenic RNA betacoronavirus. Like other RNA viruses, SARS-CoV-2 continues to evolve with or without drug selection pressure, and many variants have emerged since the beginning of the pandemic. The papain-like protease, PL ^pro, is a cysteine protease that cleaves viral polyproteins as well as ubiquitin and ISG15 modifications from host proteins. Leveraging our recently discovered Val70 ^Ub binding site in PL ^pro, we designed covalent PL ^pro inhibitors by connecting cysteine reactive warheads to the biarylphenyl PL ^pro inhibitors via flexible linkers. Several leads displayed potent enzymatic inhibition (IC ₅₀ = 0.1-0.3 μM) and antiviral activity (EC ₅₀ = 0.09-0.96 μM). Fumaramide inhibitors Jun13567 (15) , Jun13728 (16) , and Jun13714 (18) showed favorable in vivo pharmacokinetic properties with intraperitoneal injection. The X-ray crystal structure of PL ^pro with Jun13567 (15) validated our design strategy, revealing covalent conjugation between the catalytic Cys111 and the fumaramide warhead. The results suggest these covalent PL ^pro inhibitors are promising SARS-CoV-2 antiviral drug candidates.

Organizational Affiliation

Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States.

Macromolecule Content

Total Structure Weight: 74.32 kDa
Atom Count: 4,942
Modeled Residue Count: 598
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	318	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A6J (Subject of Investigation/LOI) Query on A1A6J Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain O [auth B]	C [auth A], O [auth B]	2-(3-{2-[4-(3,3-dimethylazetidin-1-yl)-4-oxobutanoyl]hydrazin-1-yl}-3-oxopropyl)-N-{(1R)-1-[(3P,5P)-3-(1-ethyl-1H-pyrazol-3-yl)-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}benzamide C₃₆ H₄₄ N₈ O₄ RZEHDNPIDQHEJC-XMMPIXPASA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
DTT Query on DTT 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]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain V [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain V [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain V [auth B]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], U [auth B], V [auth B], W [auth B], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]