9HC1 | pdb_00009hc1

SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-N-[4-(2-oxopyrrolidin-1-yl)phenyl]indane-1-carboxamide

PDB DOI: https://doi.org/10.2210/pdb9HC1/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-08 Released: 2024-11-27
Deposition Author(s): Hanoulle, X., Charton, J., Deprez, B.
Funding Organization(s): European Union (EU), Centre National de la Recherche Scientifique (CNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.220 (Depositor), 0.224 (DCC)
R-Value Work:
0.181 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-N-[4-(2-oxopyrrolidin-1-yl)phenyl]indane-1-carboxamide

Hanoulle, X., Charton, J., Deprez, B.

To be published.

Macromolecule Content

Total Structure Weight: 68.94 kDa
Atom Count: 5,485
Modelled 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, 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 LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ITP (Subject of Investigation/LOI) Query on A1ITP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	(1~{R})-~{N}-(3-chlorophenyl)-3-oxidanylidene-~{N}-[4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]-1,2-dihydroindene-1-carboxamide C₂₆ H₂₁ Cl N₂ O₃ QHXYLNDXNZHBPZ-HSZRJFAPSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], J [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	F [auth A], G [auth A], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]