The crystal structure of COVID-19 main protease in complex with an inhibitor 11b

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.

Dai, W.Zhang, B.Jiang, X.M.Su, H.Li, J.Zhao, Y.Xie, X.Jin, Z.Peng, J.Liu, F.Li, C.Li, Y.Bai, F.Wang, H.Cheng, X.Cen, X.Hu, S.Yang, X.Wang, J.Liu, X.Xiao, G.Jiang, H.Rao, Z.Zhang, L.K.Xu, Y.Yang, H.Liu, H.

(2020) Science 368: 1331-1335

  • DOI: https://doi.org/10.1126/science.abb4489
  • Primary Citation of Related Structures:  
    6LZE, 6M0K

  • PubMed Abstract: 

    SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the etiological agent responsible for the global COVID-19 (coronavirus disease 2019) outbreak. The main protease of SARS-CoV-2, M pro , is a key enzyme that plays a pivotal role in mediating viral replication and transcription. We designed and synthesized two lead compounds ( 11a and 11b ) targeting M pro Both exhibited excellent inhibitory activity and potent anti-SARS-CoV-2 infection activity. The x-ray crystal structures of SARS-CoV-2 M pro in complex with 11a or 11b , both determined at a resolution of 1.5 angstroms, showed that the aldehyde groups of 11a and 11b are covalently bound to cysteine 145 of M pro Both compounds showed good pharmacokinetic properties in vivo, and 11a also exhibited low toxicity, which suggests that these compounds are promising drug candidates.

  • Organizational Affiliation

    State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase304Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FJC

Download Ideal Coordinates CCD File 
F [auth A]~{N}-[(2~{S})-3-(3-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
C25 H25 F N4 O4
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
C2 H6 O S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.152α = 90
b = 81.701β = 114.69
c = 51.669γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina2017YFC0840300
National Natural Science Foundation of China (NSFC)China81520108019

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 2.0: 2020-05-27
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2020-06-03
    Changes: Structure summary
  • Version 2.2: 2020-06-10
    Changes: Structure summary
  • Version 2.3: 2020-07-01
    Changes: Database references
  • Version 2.4: 2021-03-10
    Changes: Structure summary
  • Version 2.5: 2023-11-29
    Changes: Data collection, Database references, Refinement description