9HDJ | pdb_00009hdj

SARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one

• PDB DOI: https://doi.org/10.2210/pdb9HDJ/pdb

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


• Deposited: 2024-11-12 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.281 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

SARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one

Hanoulle, X., Charton, J., Deprez, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 68.61 kDa 
• Atom Count: 4,900 
• Modeled Residue Count: 606 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IT1 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(3~{R})-3-[(3~{R})-3-phenyl-4-(phenylmethyl)piperazin-1-yl]carbonyl-2,3-dihydroinden-1-one C27 H26 N2 O2 UTDHFZWVCNRNGD-RPBOFIJWSA-N
FMT	E [auth B], F [auth B], G [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.281 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.883	α = 90
b = 53.858	β = 100.269
c = 115.296	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
MxCuBE	data collection
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Hanoulle, X., Charton, J., Deprez, B.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	REACT-EU 22003061
Centre National de la Recherche Scientifique (CNRS)	France	COVID and ViroCrib programs

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release