8UVM

SARS-CoV-2 papain-like protease (PLpro) complex with covalent inhibitor Jun11313

PDB DOI: https://doi.org/10.2210/pdb8UVM/pdb

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

Deposited: 2023-11-03 Released: 2024-04-03
Deposition Author(s): Ansari, A., Tan, B., Chopra, A., 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: 2.85 Å
R-Value Free: 0.204
R-Value Work: 0.178
R-Value Observed: 0.180

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model.

Tan, B., Zhang, X., Ansari, A., Jadhav, P., Tan, H., Li, K., Chopra, A., Ford, A., Chi, X., Ruiz, F.X., Arnold, E., Deng, X., Wang, J.

(2024) Science 383: 1434-1440

PubMed: 38547259 Search on PubMed
DOI: https://doi.org/10.1126/science.adm9724
Primary Citation of Related Structures:
8UOB, 8UUF, 8UUG, 8UUH, 8UUU, 8UUV, 8UUW, 8UUY, 8UVM

PubMed Abstract:
The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PL ^pro) is a promising but challenging drug target. We designed and synthesized 85 noncovalent PL ^pro inhibitors that bind to a recently discovered ubiquitin binding site and the known BL2 groove pocket near the S4 subsite. Leads inhibited PL ^pro with the inhibitory constant K _i values from 13.2 to 88.2 nanomolar. The co-crystal structures of PL ^pro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC ₅₀ from 0.44 to 2.02 micromolar. Oral treatment with Jun12682 improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting that PL ^pro inhibitors are promising oral SARS-CoV-2 antiviral candidates.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 146.68 kDa
Atom Count: 10,149
Modelled Residue Count: 1,258
Deposited Residue Count: 1,272
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, C, D	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
Y3R (Subject of Investigation/LOI) Query on Y3R Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain I [auth B]	E [auth A], I [auth B], M [auth C], Q [auth D]	ethyl 4-oxo-4-(2-{3-[2-({(1S)-1-[(3P)-3-(thiophen-3-yl)phenyl]ethyl}carbamoyl)phenyl]propanoyl}hydrazinyl)butanoate C₂₈ H₃₁ N₃ O₅ S VCEOCCSGIGLDNU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A], J [auth B], N [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D]	H [auth A], L [auth B], P [auth C], U [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	G [auth A], K [auth B], O [auth C], S [auth D], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D]