8R7B | pdb_00008r7b

SARS-CoV-2 NSP14 in complex with SAH and TDI-015051

• PDB DOI: https://doi.org/10.2210/pdb8R7B/pdb

• Classification: VIRAL PROTEIN
• Organism(s): SARS-CoV-2 pseudovirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-24 Released: 2024-10-23 
• Deposition Author(s): Meyer, C., Garzia, A., Miller, M., Huggins, D.J., Myers, R.W., Liverton, N., Kargman, S., Nitsche, J., Ganichkin, O., Steinbacher, S., Meinke, P.T., Tuschl, T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Small-molecule inhibition of SARS-CoV-2 NSP14 RNA cap methyltransferase.

Meyer, C., Garzia, A., Miller, M.W., Huggins, D.J., Myers, R.W., Hoffmann, H.H., Ashbrook, A.W., Jannath, S.Y., Liverton, N., Kargman, S., Zimmerman, M., Nelson, A.M., Sharma, V., Dolgov, E., Cangialosi, J., Penalva-Lopez, S., Alvarez, N., Chang, C.W., Oswal, N., Gonzalez, I., Rasheed, R., Goldgirsh, K., Davis, J.A., Ramos-Espiritu, L., Menezes, M.R., Larson, C., Nitsche, J., Ganichkin, O., Alwaseem, H., Molina, H., Steinbacher, S., Glickman, J.F., Perlin, D.S., Rice, C.M., Meinke, P.T., Tuschl, T.

(2025) Nature 637: 1178-1185

• PubMed: 39663451 
• DOI: https://doi.org/10.1038/s41586-024-08320-0
• Primary Citation Related Structures: 
  8R7B


• PubMed Abstract: 
  

  Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ¹ . The rapid development of highly effective vaccines ^2,3 against SARS-CoV-2 has altered the trajectory of the pandemic, and antiviral therapeutics ⁴ have further reduced the number of COVID-19 hospitalizations and deaths. Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that encode various structural and non-structural proteins, including those critical for viral RNA replication and evasion from innate immunity ⁵ . Here we report the discovery and development of a first-in-class non-covalent small-molecule inhibitor of the viral guanine-N7 methyltransferase (MTase) NSP14. High-throughput screening identified RU-0415529, which inhibited SARS-CoV-2 NSP14 by forming a unique ternary S-adenosylhomocysteine (SAH)-bound complex. Hit-to-lead optimization of RU-0415529 resulted in TDI-015051 with a dissociation constant (K _d ) of 61 pM and a half-maximal effective concentration (EC ₅₀ ) of 11 nM, inhibiting virus infection in a cell-based system. TDI-015051 also inhibited viral replication in primary small airway epithelial cells and in a transgenic mouse model of SARS CoV-2 infection with an efficacy comparable with the FDA-approved reversible covalent protease inhibitor nirmatrelvir ⁶ . The inhibition of viral cap methylases as an antiviral strategy is also adaptable to other pandemic viruses.

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Organizational Affiliation: 
• Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA.
Sanders Tri-Institutional Therapeutics Discovery Institute, The Rockefeller University, New York, NY, USA.
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.
Department of Medicine, Division of Infectious Diseases, Columbia University, New York, NY, USA.
Fisher Drug Discovery Resource Center, The Rockefeller University, New York, NY, USA.
PROTEROS Biostructures GmbH, Planegg-Martinsried, Germany.
Proteomics Resource Center, The Rockefeller University, New York, NY, USA.
Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 122.53 kDa 
• Atom Count: 7,252 
• Modeled Residue Count: 858 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine-N7 methyltransferase nsp14	A, B	528	SARS-CoV-2 pseudovirus	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.1.1.56 (PDB Primary Data), 3.1.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YDT (Subject of Investigation/LOI)	J [auth A], X [auth B]	N-[(5-fluoranyl-1-benzofuran-4-yl)methyl]-1,5-dimethyl-4-(1,4,6,7-tetrahydropyrazolo[4,3-c]pyridin-5-ylsulfonyl)pyrrole-2-carboxamide C22 H22 F N5 O4 S YVXDXTXKLFZFOI-UHFFFAOYSA-N
SAH	F [auth A], Q [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
IMD	I [auth A], N [auth B], O [auth B], P [auth B], W [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	R [auth B], S [auth B], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.448	α = 90
b = 101.071	β = 108.43
c = 90.472	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
STARANISO	data scaling
REFMAC	refinement
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Meyer, C., Garzia, A., Miller, M., Huggins, D.J., Myers, R.W., Liverton, N., Kargman, S., Nitsche, J., Ganichkin, O., Steinbacher, S., Meinke, P.T., Tuschl, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI171401
Other private	United States	--

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release
  
• Version 1.1: 2024-12-18
  Changes: Database references
• Version 1.2: 2024-12-25
  Changes: Database references
• Version 1.3: 2025-02-05
  Changes: Database references