7XAX | pdb_00007xax

Crystal structure of SARS coronavirus main protease in complex with Baicalei

PDB DOI: https://doi.org/10.2210/pdb7XAX/pdb

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

Deposited: 2022-03-19 Released: 2023-03-22
Deposition Author(s): Zhou, X.L., Li, J., Zhang, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of SARS-CoV 3C-like protease with baicalein.

Feng, J., Li, D., Zhang, J., Yin, X., Li, J.

(2022) Biochem Biophys Res Commun 611: 190-194

PubMed: 35490659 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.bbrc.2022.04.086
Primary Citation of Related Structures:
7XAX

PubMed Abstract:
The 3C-like protease (M ^pro, 3CL ^pro) plays a key role in the replication process in coronaviruses (CoVs). The M ^pro is an essential enzyme mediates CoVs replication and is a promising target for development of antiviral drugs. Until now, baicalein has been shown the specific activity for SARS-CoV M ^pro in vitro experiments. In this study, we resolved the SARS-CoV M ^pro with baicalein by X-ray diffraction at 2.25 Å (PDB code 7XAX), which provided a structural basis for the research and development of baicalein as an anti-CoVs drug.

Organizational Affiliation

Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, 110142, China.

Macromolecule Content

Total Structure Weight: 68.02 kDa
Atom Count: 4,435
Modelled Residue Count: 594
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0 EC: 3.4.22.69
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7 Go to UniProtKB: P0C6X7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C6X7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3WL (Subject of Investigation/LOI) Query on 3WL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one C₁₅ H₁₀ O₅ FXNFHKRTJBSTCS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]