9PUY | pdb_00009puy

SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 27

PDB DOI: https://doi.org/10.2210/pdb9PUY/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-07-31 Released: 2026-01-21
Deposition Author(s): Taylor, A.J., Rietz, T., Fesik, S.W.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.205 (Depositor), 0.204 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (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

Discovery of Fragment-Based Inhibitors of SARS-CoV-2 PL Pro .

Wei, Q., Taylor, A.J., Barmade, M.A., Teuscher, K.B., Chowdhury, S., Apakama, C., Anderson-Daniels, J., Yongqing, Z., Schultz, D.C., Rietz, T.A., South, T.M., Crow, M.M., Zhao, B., Amporndanai, K., Sensintaffar, J.L., Phan, J., Cherry, S., Denison, M., Lee, T., Fesik, S.W.

(2026) J Med Chem 69: 1419-1433

PubMed: 41521555 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c02832
Primary Citation Related Structures:
9PUH, 9PUJ, 9PUY, 9PV6, 9PV9, 9PVI, 9PVK

PubMed Abstract:
SARS-CoV-2 papain-like protease (PL ^Pro) plays a key role in viral replication and the host immune response and is a promising target for developing new antiviral treatments. We previously reported a fragment-based screen to identify hits that bind to SARS-CoV-2 PL ^Pro. Here, we describe the discovery of potent PL ^Pro inhibitors by optimizing one of these hits via extensive medicinal chemistry guided by multiple X-ray structures of cocomplexes. Lead compound 46 is shown to bind to the S3 and S4 pockets with nanomolar affinity (0.4 μM) and exhibits robust cellular activity and resistance to mutation. This novel class of PL ^Pro inhibitors can potentially be used as a starting point for the development of inhibitors to combat the emergence of drug-resistant viral strains and future coronavirus outbreaks.

Organizational Affiliation

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.

Macromolecule Content

Total Structure Weight: 150.66 kDa
Atom Count: 11,722
Modeled Residue Count: 1,275
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B, C, D	326	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CLD (Subject of Investigation/LOI) Query on A1CLD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	F [auth A], J [auth B], P [auth C], S [auth D]	7,8-dimethyl-1'-[(pyridin-2-yl)methyl]spiro[[1]benzopyran-2,4'-piperidin]-4(3H)-one C₂₁ H₂₄ N₂ O₂ ZJGZEFXFZOGTNZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	G [auth A], K [auth B], L [auth B], T [auth D], U [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth D] Focus chain U [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	E [auth A], I [auth B], O [auth C], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain R [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	H [auth A], M [auth B], N [auth B], Q [auth C], V [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D]