9PAD | pdb_00009pad

Crystal structure of IBV-3CLpro with ALG-097608 (Inhibitor 1)

• PDB DOI: https://doi.org/10.2210/pdb9PAD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Infectious bronchitis virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-25 Released: 2026-02-11 
• Deposition Author(s): Reddem, E.R., Forouhad, F., Shapiro, L., Stoycheva, A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.187 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structural basis for pan-coronavirus inhibition of 3CL protease

Reddem, E.R., Forouhad, F., Shapiro, L., Stoycheva, A.

(null) Structure 2026

• DOI: https://doi.org/10.1016/j.str.2026.01.003

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: 68.04 kDa 
• Atom Count: 5,632 
• Modeled Residue Count: 613 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1ab polyprotein	A, B	307	Infectious bronchitis virus	Mutation(s): 0  Gene Names: 1ab
UniProt
Find proteins for A0A1P8SSX4 (Infectious bronchitis virus) Explore A0A1P8SSX4  Go to UniProtKB:  A0A1P8SSX4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CHF (Subject of Investigation/LOI)	C [auth A], D [auth B]	(1R,2R,3S,6S,7S)-4-[(2S)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-10,10-difluoro-N-{(1E,2R)-1-imino-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-4-azatricyclo[5.2.1.0~2,6~]decane-3-carboxamide (non-preferred name) C25 H32 F5 N5 O4 BVAKDPSOHPXNPO-MPZOXFIESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.187 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.355	α = 90
b = 101.355	β = 90
c = 162.834	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Reddem, E.R., Forouhad, F., Shapiro, L., Stoycheva, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	MAVDA-1U19AI1711401
Bill & Melinda Gates Foundation	United States	INV-016167

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release