13PX | pdb_000013px

PanDDA analysis group deposition -- Crystal structure of PLpro-C111S in complex with Fr13634

• PDB DOI: https://doi.org/10.2210/pdb13PX/pdb
• Deposition Group: G_1002354 (changed state) | Explore  G_1002354  

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-09-17 Released: 2026-02-18 
• Deposition Author(s): Wang, W., Huang, L., Xu, Q., Zhu, Z., Li, M., Zhou, H., Han, T., Zheng, S., Wang, Q., Yu, F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.230 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystallographic fragment screening discovers novel micromolar active inhibitors and druggable hotspots of SARS-CoV-2 PL pro.

Wang, W.W., Huang, L.Q., Xu, Q., Zhu, Z.M., Li, M., Zhou, H., Han, T.L., Zheng, S.H., Li, J., Wang, Q.S., Yu, F.

(2026) Int J Biol Macromol 347: 150689-150689

• PubMed: 41638277 
• DOI: https://doi.org/10.1016/j.ijbiomac.2026.150689


• PubMed Abstract: 
  

  The COVID-19 pandemic has highlighted the need to develop broad-spectrum antiviral therapeutics targeting rapidly evolving coronaviruses. This research focuses on SARS-CoV-2 PL ^pro , a conserved viral protease that plays dual roles in viral polyprotein processing and host immune suppression. Using an integrated fragment-based drug discovery (FBDD) approach that combines high-throughput X-ray crystallography and biochemical assays, we systematically screened a diverse library of 800 fragment compounds. Structural characterization identified 129 validated binders occupying 12 distinct binding sites on PL ^pro . Remarkably, two fragments demonstrated potent micromolar inhibitory activity. Fr12895 inhibited SARS-CoV-2 PL ^pro protease activity (IC ₅₀  = 8.013 μM), as measured using the fluorogenic substrate RLRGG-AMC, while Fr12338 showed inhibition against PL ^pro deISGylase activity (IC ₅₀  = 4.5 μM), as determined with the substrate Ac-ISG15prox-Rh110MP. This provides a case for directly obtaining micromolar-active compounds through crystallographic fragment screening of a small number of random compounds. Detailed structural analysis revealed these fragments engage key functional regions including the blocking loop 2 (BL2) and ubiquitin/ISG15 binding interface through extensive hydrogen-bond networks and hydrophobic interactions. Our study reveals novel micromolar active inhibitors and druggable sites of SARS-CoV-2 PL ^pro by crystallographic fragment screening, provides crucial scaffold and a structural roadmap for developing broad-spectrum antivirals against coronaviruses.

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Organizational Affiliation: 
• Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China.
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
Jiangxi Province Key Laboratory of Pharmacology of Traditional Chinese Medicine, School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China. Electronic address: [e-mail].
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China. Electronic address: [e-mail].
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.14 kDa 
• Atom Count: 2,559 
• Modeled Residue Count: 313 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	354	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CWF (Subject of Investigation/LOI)	C [auth A], D [auth A]	4-aminobenzamide C7 H8 N2 O QIKYZXDTTPVVAC-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.230 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.32	α = 90
b = 82.32	β = 90
c = 134.28	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
DIMPLE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-18 
Deposition Author(s): Wang, W., Huang, L., Xu, Q., Zhu, Z., Li, M., Zhou, H., Han, T., Zheng, S., Wang, Q., Yu, F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32471251

Revision History  

• Version 1.0: 2026-02-18
  Type: Initial release