6XA4

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with UAW241


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and inhibition of the SARS-CoV-2 main protease reveals strategy for developing dual inhibitors against M pro and cathepsin L.

Sacco, M.D.Ma, C.Lagarias, P.Gao, A.Townsend, J.A.Meng, X.Dube, P.Zhang, X.Hu, Y.Kitamura, N.Hurst, B.Tarbet, B.Marty, M.T.Kolocouris, A.Xiang, Y.Chen, Y.Wang, J.

(2020) Sci Adv 

  • DOI: 10.1126/sciadv.abe0751
  • Primary Citation of Related Structures:  
    6XA4, 6XBI, 6XBH, 6XBG, 6XFN

  • PubMed Abstract: 
  • The main protease (M pro ) of SARS-CoV-2 is a key antiviral drug target. While most M pro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently discovered several M pro inhibitors have hydro ...

    The main protease (M pro ) of SARS-CoV-2 is a key antiviral drug target. While most M pro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently discovered several M pro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II and XII, which are also active against human cathepsin L, a host-protease that is important for viral entry. In this study, we solved X-ray crystal structures of M pro in complex with calpain inhibitors II and XII, and three analogs of GC-376 The structure of M pro with calpain inhibitor II confirmed the S1 pocket can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. Interestingly, the structure of calpain inhibitor XII revealed an unexpected, inverted binding pose. Taken together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of dual inhibitors as SARS-CoV-2 antivirals.


    Organizational Affiliation

    Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, 85721, USA junwang@pharmacy.arizona.edu ychen1@usf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
main proteaseA308Severe 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)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
inhibitor UAW241B4synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002391
Query on PRD_002391
Bcovalently bound calpain inhibitor IIOligopeptide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.538α = 90
b = 54.204β = 100.71
c = 45.414γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references