9OT4 | pdb_00009ot4

SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor E9

PDB DOI: https://doi.org/10.2210/pdb9OT4/pdb

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

Deposited: 2025-05-26 Released: 2026-06-24
Deposition Author(s): Mazzorana, M., Oliveira Borges, P.H., Silva-Junior, F., Baptista Ferreira, S., Walsh, M.A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.226 (Depositor), 0.228 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor E2

Mazzorana, M., Oliveira Borges, P.H., Silva-Junior, F., Baptista Ferreira, S., Walsh, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 68.11 kDa
Atom Count: 4,886
Modeled Residue Count: 600
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CD9 (Subject of Investigation/LOI) Query on A1CD9 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1-(8-methyl-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)ethan-1-one C₁₄ H₁₆ N₂ O KEKBLSZOFATKIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.226 (Depositor), 0.228 (DCC)
R-Value Work: 0.191 (Depositor), 0.192 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.82	α = 90
b = 99.305	β = 90
c = 103.252	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Oliveira Borges, P.H.

Silva-Junior, F.

Baptista Ferreira, S.

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2026-06-24
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.