7BUY

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

• PDB DOI: https://doi.org/10.2210/pdb7BUY/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-08 Released: 2020-04-29 
• Deposition Author(s): Zhao, Y., Zhang, B., Jin, Z., Liu, X., Yang, H., Rao, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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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 

Starting Model: experimental

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 27: 529-532

• PubMed: 32382072 
• DOI: https://doi.org/10.1038/s41594-020-0440-6
• Primary Citation of Related Structures:  
  7BUY


• 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 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.

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Organizational Affiliation: 

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,597 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JRY (Subject of Investigation/LOI)	B [auth A]	hexylcarbamic acid C7 H15 N O2 YAQPZDICKJDHTR-UHFFFAOYSA-N
DMS (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

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 = 98.028	α = 90
b = 81.652	β = 114.88
c = 51.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Zhao, Y., Zhang, B., Jin, Z., Liu, X., Yang, H., Rao, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81520108019
National Natural Science Foundation of China (NSFC)	China	813300237

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-20
  Changes: Database references
• Version 1.2: 2020-06-24
  Changes: Database references
• Version 1.3: 2021-02-17
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description