7TFR | pdb_00007tfr

Room temperature X-ray structure of SARS-CoV-2 main protease (3CL Mpro) in complex with NBH-2

• PDB DOI: https://doi.org/10.2210/pdb7TFR/pdb

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


• Deposited: 2022-01-07 Released: 2022-03-02 
• Deposition Author(s): Kovalevsky, A., Kneller, D.W., Coates, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease

Kneller, D.W., Li, H., Phillips, G., Weiss, K.L., Zhang, Q., Arnould, M.A., Jonsson, C.B., Surendranathan, S., Parvathareddy, J., Blakeley, M.P., Coates, L., Louis, J.M., Bonnesen, P.V., Kovalevsky, A.

(2022) Nat Commun 13: 2268

• PubMed: 35477935 
• DOI: https://doi.org/10.1038/s41467-022-29915-z
• Primary Citation Related Structures: 
  7SI9, 7TDU, 7TEH, 7TFR


• PubMed Abstract: 
  

  Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (M ^pro ) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the M ^pro /BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor's keto-warhead creates a negatively charged oxyanion. Protonation states of the ionizable residues in the M ^pro active site adapt to the inhibitor, which appears to be an intrinsic property of M ^pro . Structural comparisons of the hybrid inhibitors with PF-07321332 reveal unconventional F···O interactions of PF-07321332 with M ^pro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals.

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Organizational Affiliation: 
• Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38103, USA.
Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN, USA.
Regional Biocontainment Laboratory, The University of Tennessee Health Science Center, Memphis, TN, 38105, USA.
Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000, Grenoble, France.
Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA.
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. [e-mail].
Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. [e-mail].

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: 34.49 kDa 
• Atom Count: 2,594 
• 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
NB2 (Subject of Investigation/LOI)	B [auth A]	(1R,2S,5S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-({1-[(2-methylpropane-2-sulfonyl)methyl]cyclohexyl}carbamoyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C33 H56 N6 O6 S RXHKWDZUWDFTBO-TWNGUQAKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.991	α = 90
b = 80.969	β = 96.88
c = 88.656	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Kovalevsky, A., Kneller, D.W., Coates, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary