6LU7

The crystal structure of COVID-19 main protease in complex with an inhibitor N3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Structure of Mprofrom SARS-CoV-2 and discovery of its inhibitors.

Jin, Z.Du, X.Xu, Y.Deng, Y.Liu, M.Zhao, Y.Zhang, B.Li, X.Zhang, L.Peng, C.Duan, Y.Yu, J.Wang, L.Yang, K.Liu, F.Jiang, R.Yang, X.You, T.Liu, X.Yang, X.Bai, F.Liu, H.Liu, X.Guddat, L.W.Xu, W.Xiao, G.Qin, C.Shi, Z.Jiang, H.Rao, Z.Yang, H.

(2020) Nature 582: 289-293

  • DOI: 10.1038/s41586-020-2223-y
  • Primary Citation of Related Structures:  
    7BQY, 6LU7

  • PubMed Abstract: 
  • A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the aetiological agent responsible for the 2019-2020 viral pneumonia outbreak of coronavirus disease 2019 (COVID-19) 1-4 . Currently, there are no targeted therapeutic agents for the treatment of this disease, and effective treatment options remain very limited ...

    A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the aetiological agent responsible for the 2019-2020 viral pneumonia outbreak of coronavirus disease 2019 (COVID-19) 1-4 . Currently, there are no targeted therapeutic agents for the treatment of this disease, and effective treatment options remain very limited. Here we describe the results of a programme that aimed to rapidly discover lead compounds for clinical use, by combining structure-assisted drug design, virtual drug screening and high-throughput screening. This programme focused on identifying drug leads that target main protease (M pro ) of SARS-CoV-2: M pro is a key enzyme of coronaviruses and has a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-2 5,6 . We identified a mechanism-based inhibitor (N3) by computer-aided drug design, and then determined the crystal structure of M pro of SARS-CoV-2 in complex with this compound. Through a combination of structure-based virtual and high-throughput screening, we assayed more than 10,000 compounds-including approved drugs, drug candidates in clinical trials and other pharmacologically active compounds-as inhibitors of M pro . Six of these compounds inhibited M pro , showing half-maximal inhibitory concentration values that ranged from 0.67 to 21.4 μM. One of these compounds (ebselen) also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of our screening strategy, which can lead to the rapid discovery of drug leads with clinical potential in response to new infectious diseases for which no specific drugs or vaccines are available.


    Related Citations: 
    • Structure of Mpro from COVID-19 virus and discovery of its inhibitors.
      Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., Yang, X., Bai, F., Liu, H., Liu, X., Guddat, L., Xu, W., Xiao, G., Qin, C., Shi, Z., Jiang, H., Rao, Z., Yang, H.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. yanght@shanghaitech.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinase A306Severe 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
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE C6synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.931α = 90
b = 79.477β = 114.55
c = 51.803γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 2.0: 2020-02-12
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2020-02-19
    Changes: Database references, Structure summary
  • Version 2.2: 2020-02-26
    Changes: Data collection
  • Version 2.3: 2020-03-11
    Changes: Source and taxonomy, Structure summary
  • Version 2.4: 2020-03-18
    Changes: Database references
  • Version 2.5: 2020-04-22
    Changes: Database references
  • Version 2.6: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 2.7: 2020-05-27
    Changes: Database references
  • Version 2.8: 2020-06-10
    Changes: Structure summary
  • Version 2.9: 2020-06-24
    Changes: Database references
  • Version 3.0: 2020-07-29
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.1: 2021-03-10
    Changes: Structure summary