7LB7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.204 

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

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1021/acs.jmedchem.1c00058
  • Primary Citation of 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 ...

    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 .


    Related Citations: 
    • Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
      Adams, P.D., Mustyakimov, M., Afonine, P.V., Langan, P.
      (2009) Acta Crystallogr D Biol Crystallogr 65: 567

    Organizational Affiliation

    National Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SV6
Query on SV6

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002448 (SV6)
Query on PRD_002448
B [auth A]TELAPREVIR, bound formPeptide-like / Antiviral Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.558α = 90
b = 55.691β = 101.31
c = 48.808γ = 90
Software Package:
Software NamePurpose
nCNSrefinement
PHASERphasing
CrysalisProdata reduction
CrysalisProdata scaling
Mantiddata reduction
LAUENORMdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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