8EOY

Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI37

PDB DOI: https://doi.org/10.2210/pdb8EOY/pdb

Classification: VIRAL PROTEIN,HYDROLASE/INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-04 Released: 2023-10-11
Deposition Author(s): Yang, K.S., Liu, W.R.
Funding Organization(s): Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.299
R-Value Work: 0.236
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the SARS-CoV-2 main protease in complex with inhibitors

Yang, K.S., Sankaran, B., Liu, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 68.57 kDa
Atom Count: 5,053
Modelled Residue Count: 612
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	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WOH Query on WOH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	benzyl {(2S)-1-[2-(3-amino-3-oxopropyl)-2-(chloroacetyl)hydrazinyl]-4-methyl-1-oxopentan-2-yl}carbamate (non-preferred name) C₁₉ H₂₇ Cl N₄ O₅ SEDQMDCLDZNPIX-HNNXBMFYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.299
R-Value Work: 0.236
R-Value Observed: 0.239
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.234	α = 91.08
b = 60.751	β = 108.98
c = 67.65	γ = 107.79

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Welch Foundation	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-10-11
Type: Initial release
Version 1.1: 2023-11-15
Changes: Data collection
Version 1.2: 2024-10-23
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.