ISDA: 9U7D

Deposition Date 2025-03-24

Release Date 2025-12-24

Last Version Date 2026-07-08

Entry Detail

PDB ID:

9U7D

Keywords:

VIRAL PROTEIN

Title:

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

Biological Source:

Source Organism(s):

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.70 Å

R-Value Free:

0.23

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

I 41 2 2

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Papain-like protease nsp3
Gene (Uniprot):rep
Mutagens:C111S
Chain IDs:A
Chain Length:312
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTD1 Pfam ID:PF08715 EC:2.7.7.48

Ligand Molecules

A1EOE

PEG

Primary Citation

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.Show

Nat Commun 17 ? ? (2026)

PMID: 41587976 DOI: 10.1038/s41467-026-68795-5

Primary Citation of related structures

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