7BUY

The crystal structure of COVID-19 main protease in complex with carmofur


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur.

Jin, Z.Zhao, Y.Sun, Y.Zhang, B.Wang, H.Wu, Y.Zhu, Y.Zhu, C.Hu, T.Du, X.Duan, Y.Yu, J.Yang, X.Yang, X.Yang, K.Liu, X.Guddat, L.W.Xiao, G.Zhang, L.Yang, H.Rao, Z.

(2020) Nat Struct Mol Biol 

  • DOI: 10.1038/s41594-020-0440-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The antineoplastic drug carmofur is shown to inhibit the SARS-CoV-2 main protease (M pro ). Here, the X-ray crystal structure of M pro in complex with carmofur reveals that the carbonyl reactive group of carmofur is covalently ...

    The antineoplastic drug carmofur is shown to inhibit the SARS-CoV-2 main protease (M pro ). Here, the X-ray crystal structure of M pro in complex with carmofur reveals that the carbonyl reactive group of carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC 50  = 24.30 μM) and is a promising lead compound to develop new antiviral treatment for COVID-19.


    Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SARS-CoV-2 virus Main protease
A
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JRY
Query on JRY

Download CCD File 
A
hexylcarbamic acid
C7 H15 N O2
YAQPZDICKJDHTR-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.028α = 90
b = 81.652β = 114.88
c = 51.639γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81520108019
National Natural Science Foundation of China (NSFC)China813300237

Revision History 

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references