8GFO

Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304, in complex with GC373


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.

Kovalevsky, A.Aniana, A.Coates, L.Bonnesen, P.V.Nashed, N.T.Louis, J.M.

(2023) J Biol Chem 299: 104886-104886

  • DOI: https://doi.org/10.1016/j.jbc.2023.104886
  • Primary Citation of Related Structures:  
    8GFK, 8GFN, 8GFO, 8GFR, 8GFU

  • PubMed Abstract: 

    The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MPro WT ) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373), and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is ∼400-fold weaker corresponding to 3.5 kcal/mol and 13.3 °C decrease in free energy (ΔG) and thermal stability (T m ), respectively, relative to MPro WT . The H41A mutation results in a 20-fold increase in the dissociation constant (K d ), and 1.7 kcal/mol and 1.4 °C decreases in ΔG and T m , respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MPro H41A , whereas no significant change is observed in binding to MPro WT . Structures of the four inhibitor complexes with MPro 1-304/C145A show that the active site geometries of the complexes are nearly identical to that of MPro WT with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MPro WT that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MPro C145A also results in a significant, but smaller, increase in K d and decrease in ΔG and T m , relative to NMV.


  • Organizational Affiliation

    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA. Electronic address: kovalevskyay@ornl.gov.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5304Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZH0 (Subject of Investigation/LOI)
Query on ZH0

Download Ideal Coordinates CCD File 
B [auth A]N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
C21 H29 N3 O5
QYENXTYKACLCGO-BZSNNMDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.274α = 90
b = 81.931β = 95.3
c = 91.656γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection