7LB7 | pdb_00007lb7

Joint X-ray/neutron structure of SARS-CoV-2 main protease (3CL Mpro) in complex with Telaprevir

• PDB DOI: https://doi.org/10.2210/pdb7LB7/pdb

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


• Deposited: 2021-01-07 Released: 2021-01-20 
• Deposition Author(s): Kovalevsky, A.Y., Kneller, D.W., Coates, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.198 (DCC) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.228 (Depositor) 
• R-Value Work: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography.

Kneller, D.W., Phillips, G., Weiss, K.L., Zhang, Q., Coates, L., Kovalevsky, A.

(2021) J Med Chem 64: 4991-5000

• PubMed: 33755450 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c00058
• Primary Citation Related Structures: 
  7LB7


• PubMed Abstract: 
  

  The main protease (3CL M ^pro ) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is an essential enzyme for viral replication with no human counterpart, making it an attractive drug target. To date, no small-molecule clinical drugs are available that specifically inhibit SARS-CoV-2 M ^pro . To aid rational drug design, we determined a neutron structure of M ^pro in complex with the α-ketoamide inhibitor telaprevir at near-physiological (22 °C) temperature. We directly observed protonation states in the inhibitor complex and compared them with those in the ligand-free M ^pro , revealing modulation of the active-site protonation states upon telaprevir binding. We suggest that binding of other α-ketoamide covalent inhibitors can lead to the same protonation state changes in the M ^pro active site. Thus, by studying the protonation state changes induced by inhibitors, we provide crucial insights to help guide rational drug design, allowing precise tailoring of inhibitors to manipulate the electrostatic environment of SARS-CoV-2 M ^pro .

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Organizational Affiliation: 
• Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States.
National Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States.
Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States.

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: 34.51 kDa 
• Atom Count: 2,512 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SV6	B [auth A]	(1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide C36 H55 N7 O6 FTZGWEAUHOMNIG-FJRGXGLZSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002448 (SV6)	B [auth A]	TELAPREVIR, bound form	Peptide-like / Antiviral

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.198 (DCC) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.228 (Depositor) 
• R-Value Work:  0.216 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.558	α = 90
b = 55.691	β = 101.31
c = 48.808	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
PHASER	phasing
CrysalisPro	data reduction
CrysalisPro	data scaling
Mantid	data reduction
LAUENORM	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Kovalevsky, A.Y., Kneller, D.W., Coates, L.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-04-21
  Changes: Database references
• Version 1.2: 2021-05-05
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Refinement description, Source and taxonomy
• Version 1.4: 2024-04-03
  Changes: Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary