9RIY | pdb_00009riy

SARS-CoV-2 with a bound inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9RIY/pdb

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


• Deposited: 2025-06-12 Released: 2025-07-09 
• Deposition Author(s): Mac Sweeney, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 

Starting Model: experimental

Literature

SARS-CoV-2 with a bound inhibitor

Mac Sweeney, A.

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: 68.48 kDa 
• Atom Count: 4,938 
• Modeled Residue Count: 605 
• 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  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JGM (Subject of Investigation/LOI)	C [auth A], E [auth B]	[6-(4-iodanylphenoxy)pyrimidin-4-yl]methanimine C11 H8 I N3 O JDKLMVUMEZXJLE-AWNIVKPZSA-N
DMS	D [auth A], F [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.76	α = 90
b = 99.54	β = 90
c = 103.52	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Mac Sweeney, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release