7KX5

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with noncovalent inhibitor Jun8-76-3A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity.

Ma, C.Xia, Z.Sacco, M.D.Hu, Y.Townsend, J.A.Meng, X.Choza, J.Tan, H.Jang, J.Gongora, M.V.Zhang, X.Zhang, F.Xiang, Y.Marty, M.T.Chen, Y.Wang, J.

(2021) J Am Chem Soc 143: 20697-20709

  • DOI: 10.1021/jacs.1c08060
  • Primary Citation of Related Structures:  
    7KX5, 7RN0, 7RN1

  • PubMed Abstract: 
  • The main protease (M pro ) is a validated antiviral drug target of SARS-CoV-2. A number of M pro inhibitors have now advanced to animal model study and human clinical trials. However, one issue yet to be addressed is the target selectivity over host proteases such as cathepsin L ...

    The main protease (M pro ) is a validated antiviral drug target of SARS-CoV-2. A number of M pro inhibitors have now advanced to animal model study and human clinical trials. However, one issue yet to be addressed is the target selectivity over host proteases such as cathepsin L. In this study we describe the rational design of covalent SARS-CoV-2 M pro inhibitors with novel cysteine reactive warheads including dichloroacetamide, dibromoacetamide, tribromoacetamide, 2-bromo-2,2-dichloroacetamide, and 2-chloro-2,2-dibromoacetamide. The promising lead candidates Jun9-62-2R (dichloroacetamide) and Jun9-88-6R (tribromoacetamide) had not only potent enzymatic inhibition and antiviral activity but also significantly improved target specificity over caplain and cathepsins. Compared to GC-376 , these new compounds did not inhibit the host cysteine proteases including calpain I, cathepsin B, cathepsin K, cathepsin L, and caspase-3. To the best of our knowledge, they are among the most selective covalent M pro inhibitors reported thus far. The cocrystal structures of SARS-CoV-2 M pro with Jun9-62-2R and Jun9-57-3R reaffirmed our design hypothesis, showing that both compounds form a covalent adduct with the catalytic C145. Overall, these novel compounds represent valuable chemical probes for target validation and drug candidates for further development as SARS-CoV-2 antivirals.


    Related Citations: 
    • Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors.
      Kitamura, N., Sacco, M.D., Ma, C., Hu, Y., Townsend, J.A., Meng, X., Zhang, F., Zhang, X., Ba, M., Szeto, T., Kukuljac, A., Marty, M.T., Schultz, D., Cherry, S., Xiang, Y., Chen, Y., Wang, J.
      (2022) J Med Chem 65: 2848

    Organizational Affiliation

    Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, 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), 3.1 (UniProt), 2.1.1 (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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X7V (Subject of Investigation/LOI)
Query on X7V

Download Ideal Coordinates CCD File 
B [auth A]N-([1,1'-biphenyl]-4-yl)-N-[(1R)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]furan-2-carboxamide
C32 H27 N3 O3
RYGJIKURQDMMQZ-YUDQIZAISA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.092α = 90
b = 52.106β = 103.29
c = 44.47γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI147325
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI157046

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Database references
  • Version 1.2: 2022-03-09
    Changes: Database references
  • Version 1.3: 2022-04-27
    Changes: Database references