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)

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
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Ligand Structure Quality Assessment

This is version 1.5 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 27: 529-532

PubMed: 32382072 Search on PubMed
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JRY (Subject of Investigation/LOI) Query on JRY Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	hexylcarbamic acid C₇ H₁₅ N O₂ YAQPZDICKJDHTR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS (Subject of Investigation/LOI) Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

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 (Full details and data files)

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
Version 1.5: 2024-11-06
Changes: Structure summary