9L09 | pdb_00009l09

SARS-CoV-2 C-RTC with 13-TP

• PDB DOI: https://doi.org/10.2210/pdb9L09/pdb
• NAKB: 9L09
• EM Map EMD-62692: EMDB EMDataResource

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


• Deposited: 2024-12-12 Released: 2025-03-19 
• Deposition Author(s): Huang, Y.C., Liang, L., Liu, Y.X., Yan, L.M., Lou, Z.Y., Rao, Z.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Discovery of a 2'-a-Fluoro-2'-b-C-(fluoromethyl) Purine Nucleotide Prodrug as a Potential Oral Anti-SARS-CoV-2 Agent

Liang, L., Meng, Y., Chang, X., Li, E., Huang, Y., Yan, L., Lou, Z., Peng, Y., Zhu, B., Yu, W., Chang, J.

(2025) J Med Chem 68: 1994-2007

• PubMed: 39804580 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c02769
• Primary Citation of Related Structures:  
  9L09


• PubMed Abstract: 
  

  A novel 2'-α-fluoro-2'-β- C -(fluoromethyl) purine nucleoside phosphoramidate prodrug 15 has been designed and synthesized to treat SARS-CoV-2 infection. The SARS-CoV-2 central replication transcription complex (C-RTC, nsp12-nsp7-nsp8 ₂ ) catalyzed in vitro RNA synthesis was effectively inhibited by the corresponding bioactive nucleoside triphosphate ( 13-TP ). The cryo-electron microscopy structure of the C-RTC: 13-TP complex was also determined. Compound 15 exhibited potent in vitro antiviral activity against the SARS-CoV-2 20SF107 strain (EC ₅₀ = 0.56 ± 0.06 μM) and the Omicron BA.5 variant (EC ₅₀ = 0.96 ± 0.23 μM) with low cytotoxicity. Furthermore, it was well tolerated in rats at doses of up to 2000 mg/kg, and a single oral dose of this prodrug at 40 mg/kg led to high levels of 13-TP in the target organ lungs of rats with a long half-life. These findings support the further development of compound 15 as an orally available antiviral agent for the treatment of SARS-CoV-2 infection.

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Organizational Affiliation: 
• State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China.
State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, College of Chemistry, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin 300071, China.
MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China.
Henan Key Laboratory for Pharmacology of Liver Diseases, Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 167.02 kDa 
• Atom Count: 10,489 
• Modeled Residue Count: 1,277 
• Deposited Residue Count: 1,433 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase nsp12	A	932	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.7.7.48 (PDB Primary Data), 2.7.7.50 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B, D	198	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	C	83	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*GP*AP*AP*GP*CP*UP*AP*U*(A1ELZ))-3')	E [auth I]	11	Severe acute respiratory syndrome coronavirus 2

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*AP*UP*AP*GP*CP*UP*UP*CP*UP*U)-3')	F [auth J]	11	Severe acute respiratory syndrome coronavirus 2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Huang, Y.C., Liang, L., Liu, Y.X., Yan, L.M., Lou, Z.Y., Rao, Z.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection