8R12

Structure of compound 8 bound to SARS-CoV-2 main protease

• PDB DOI: https://doi.org/10.2210/pdb8R12/pdb

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


• Deposited: 2023-11-01 Released: 2024-02-07 
• Deposition Author(s): Mac Sweeney, A., Hazemann, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.238 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches

Mac Sweeney, A., Hazemann, J.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 68.5 kDa 
• Atom Count: 5,237 
• Modelled Residue Count: 608 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

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  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XH9 (Subject of Investigation/LOI)	C [auth A], E [auth B]	2-[[4-(5-chloranylpyridin-3-yl)carbonyl-1,4-diazepan-1-yl]methyl]benzenecarbonitrile C19 H19 Cl N4 O VIHXPVLCTFBBEL-UHFFFAOYSA-N
DMS	F [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.238 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.01	α = 90
b = 100.34	β = 90
c = 104.55	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Mac Sweeney, A., Hazemann, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release