9U7D | pdb_00009u7d

Crystal structure of SARS-CoV-2 papain-like protease (Cys111Ser) in complex with YL1004

• PDB DOI: https://doi.org/10.2210/pdb9U7D/pdb

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


• Deposited: 2025-03-24 Released: 2025-12-24 
• Deposition Author(s): Zeng, R., Deng, X.Y., Yu, J., Yang, S.Y., Lei, J.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.231 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

YL1004 is a SARS-CoV-2 papain-like protease inhibitor with immunomodulatory and antiviral activity in mice.

Nan, J., Shuai, H., Qiao, J., Zeng, R., Du, L., Chen, Y., Yoon, C., Hu, J., Guo, W., Wang, L., Huang, C., Zhu, L., Li, Y., Zhang, S., Deng, X., Sun, J., Du, L., Ma, R., Huang, Q., Lei, J., Chu, H., Yang, S.

(2026) Nat Commun 17

• PubMed: 41587976 
• DOI: https://doi.org/10.1038/s41467-026-68795-5
• Primary Citation Related Structures: 
  9U7D


• PubMed Abstract: 
  

  The evolution of SARS-CoV-2, coupled with its immune evasion mechanisms, underscores the urgent need for antiviral strategies beyond vaccination. The papain-like protease (PL ^pro ) is a dual-functional enzyme essential for viral replication and suppression of host innate immunity. Here, we present the rational design and characterization of YL1004, a tricyclic oral PL ^pro inhibitor demonstrating robust, cross-variant SARS-CoV-2 antiviral activity and favorable pharmacokinetic properties. YL1004 potently inhibits the enzymatic function of PL ^pro , disrupts deubiquitination and deISGylation processes, and restores antiviral immune signaling cascades. Notably, YL1004 suppresses the replication of SARS-CoV-2 wildtype, Delta and Omicron variants. Additionally, it is also effective against the M ^pro E166V recombinant SARS-CoV-2 strain, which confers resistance to nirmatrelvir. In the lethal SARS-CoV-2 infection model using K18-hACE2 mice, YL1004 confers complete protection to animal survival, significantly reduces viral load in nasal turbinate and lung tissues, and alleviates virus-induced pathological tissue damages. Co-crystal structural analysis revealed a distinctive binding mode, enhancing target engagement through expanded hydrophobic interactive interface and additional hydrogen bonding interactions. Collectively, these findings establish YL1004 as a promising therapeutic candidate, harnessing dual antiviral and immunomodulatory mechanisms to combat SARS-CoV-2 and emerging variants.

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Organizational Affiliation: 
• Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [e-mail].
State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China. [e-mail].
Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, Hong Kong Special Administrative Region, China. [e-mail].
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [e-mail].
New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.68 kDa 
• Atom Count: 2,666 
• Modeled Residue Count: 307 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	312	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EOE (Subject of Investigation/LOI)	B [auth A]	(4~{a}~{S})-8-azanyl-3-methyl-~{N}-[1-[4-(oxan-4-ylamino)naphthalen-1-yl]cyclopropyl]-2,4,4~{a},5-tetrahydro-1~{H}-pyrazino[2,1-c][1,4]benzoxazine-9-carboxamide C31 H37 N5 O3 IFYKCXWVMYHVGS-NRFANRHFSA-N
PEG	Q [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.231 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.639	α = 90
b = 111.639	β = 90
c = 220.006	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Zeng, R., Deng, X.Y., Yu, J., Yang, S.Y., Lei, J.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC2303700
National Natural Science Foundation of China (NSFC)	China	82473844

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release
  
• Version 1.1: 2026-07-08
  Changes: Database references