9RI0 | pdb_00009ri0

SARS-CoV-2 3CL protease with a bound inhibitor

PDB DOI: https://doi.org/10.2210/pdb9RI0/pdb

Classification: HYDROLASE
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-10 Released: 2025-07-09
Deposition Author(s): Mac Sweeney, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.198 (Depositor), 0.198 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

SARS-CoV-2 3CL protease with a bound inhibitor

Mac Sweeney, A.

To be published.

Macromolecule Content

Total Structure Weight: 69.01 kDa
Atom Count: 5,427
Modeled Residue Count: 610
Deposited Residue Count: 612
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 nsp5	A [auth B], B [auth A]	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JGF (Subject of Investigation/LOI) Query on A1JGF Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain H [auth A] MOL2 format, chain C [auth B] MOL2 format, chain H [auth A] mmCIF format, chain C [auth B] mmCIF format, chain H [auth A]	C [auth B], H [auth A]	[1-[[5-chloranyl-1-(phenylmethyl)benzimidazol-2-yl]methyl]-1,2,4-triazol-3-yl]methanamine C₁₈ H₁₇ Cl N₆ AJMPAXTYEVALRO-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain H [auth A] Interactions & Density Focus chain C [auth B] Focus chain H [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain G [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain D [auth B] MOL2 format, chain G [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain D [auth B] mmCIF format, chain G [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	D [auth B], G [auth B], J [auth A], K [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain G [auth B] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain D [auth B] Focus chain G [auth B] Focus chain J [auth A] Focus chain K [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain I [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain I [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain I [auth A]	E [auth B], F [auth B], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]