8VDJ | pdb_00008vdj

Crystal structure of SARS-CoV-2 3CL protease (3CLpro) as a covalent complex with EDP-235

• PDB DOI: https://doi.org/10.2210/pdb8VDJ/pdb

• Classification: VIRAL PROTEIN,HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-15 Released: 2024-08-14 
• Deposition Author(s): Cade, I.A., Rhodin, M.H.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

The small molecule inhibitor of SARS-CoV-2 3CLpro EDP-235 prevents viral replication and transmission in vivo.

Rhodin, M.H.J., Reyes, A.C., Balakrishnan, A., Bisht, N., Kelly, N.M., Gibbons, J.S., Lloyd, J., Vaine, M., Cressey, T., Crepeau, M., Shen, R., Manalo, N., Castillo, J., Levene, R.E., Leonard, D., Zang, T., Jiang, L., Daniels, K., Cox, R.M., Lieber, C.M., Wolf, J.D., Plemper, R.K., Leist, S.R., Scobey, T., Baric, R.S., Wang, G., Goodwin, B., Or, Y.S.

(2024) Nat Commun 15: 6503-6503

• PubMed: 39090095 
• DOI: https://doi.org/10.1038/s41467-024-50931-8
• Primary Citation of Related Structures:  
  8VDJ


• PubMed Abstract: 
  

  The COVID-19 pandemic has led to the deaths of millions of people and severe global economic impacts. Small molecule therapeutics have played an important role in the fight against SARS-CoV-2, the virus responsible for COVID-19, but their efficacy has been limited in scope and availability, with many people unable to access their benefits, and better options are needed. EDP-235 is specifically designed to inhibit the SARS-CoV-2 3CLpro, with potent nanomolar activity against all SARS-CoV-2 variants to date, as well as clinically relevant human and zoonotic coronaviruses. EDP-235 maintains potency against variants bearing mutations associated with nirmatrelvir resistance. Additionally, EDP-235 demonstrates a ≥ 500-fold selectivity index against multiple host proteases. In a male Syrian hamster model of COVID-19, EDP-235 suppresses SARS-CoV-2 replication and viral-induced hamster lung pathology. In a female ferret model, EDP-235 inhibits production of SARS-CoV-2 infectious virus and RNA at multiple anatomical sites. Furthermore, SARS-CoV-2 contact transmission does not occur when naïve ferrets are co-housed with infected, EDP-235-treated ferrets. Collectively, these results demonstrate that EDP-235 is a broad-spectrum coronavirus inhibitor with efficacy in animal models of primary infection and transmission.

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Organizational Affiliation: 
• Enanta Pharmaceuticals, Inc., Watertown, MA, USA. [e-mail].
Enanta Pharmaceuticals, Inc., Watertown, MA, USA.
Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 68.79 kDa 
• Atom Count: 4,883 
• Modeled Residue Count: 598 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
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
A1AA0 (Subject of Investigation/LOI)	C [auth A], D [auth B]	4,6,7-trifluoro-N-{(2S)-1-[(3R,5'R)-5'-(iminomethyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidin]-1'-yl]-4-methyl-1-oxopentan-2-yl}-N-methyl-1H-indole-2-carboxamide C28 H28 F3 N5 O3 HTIJRVKDMBVLCG-RAAJOXOESA-N
SCN	E [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.451	α = 90
b = 99.13	β = 90
c = 100.626	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
autoPROC	data processing
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Cade, I.A., Rhodin, M.H.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary