7D3I

Crystal structure of SARS-CoV-2 main protease in complex with MI-23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model.

Qiao, J.Li, Y.S.Zeng, R.Liu, F.L.Luo, R.H.Huang, C.Wang, Y.F.Zhang, J.Quan, B.Shen, C.Mao, X.Liu, X.Sun, W.Yang, W.Ni, X.Wang, K.Xu, L.Duan, Z.L.Zou, Q.C.Zhang, H.L.Qu, W.Long, Y.H.Li, M.H.Yang, R.C.Liu, X.You, J.Zhou, Y.Yao, R.Li, W.P.Liu, J.M.Chen, P.Liu, Y.Lin, G.F.Yang, X.Zou, J.Li, L.Hu, Y.Lu, G.W.Li, W.M.Wei, Y.Q.Zheng, Y.T.Lei, J.Yang, S.

(2021) Science 371: 1374-1378

  • DOI: https://doi.org/10.1126/science.abf1611
  • Primary Citation of Related Structures:  
    7C7P, 7COM, 7D3I

  • PubMed Abstract: 

    The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continually poses serious threats to global public health. The main protease (M pro ) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing M pro inhibitors derived from either boceprevir or telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 M pro activity in vitro, with 50% inhibitory concentration values ranging from 7.6 to 748.5 nM. The cocrystal structure of M pro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a transgenic mouse model of SARS-CoV-2 infection, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.


  • Organizational Affiliation

    State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GQU (Subject of Investigation/LOI)
Query on GQU

Download Ideal Coordinates CCD File 
B [auth A](3~{S},3~{a}~{S},6~{a}~{R})-2-[3-[3,5-bis(fluoranyl)phenyl]propanoyl]-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide
C24 H29 F2 N3 O4
ZUAZJPLYYVHKFN-NAFADOBPSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.481α = 90
b = 52.456β = 103.3
c = 45.404γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2020YFS0010/HX2019nCoV039

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2021-03-10
    Changes: Structure summary
  • Version 1.3: 2021-04-14
    Changes: Database references
  • Version 1.4: 2023-11-29
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary