9PAC | pdb_00009pac

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

• PDB DOI: https://doi.org/10.2210/pdb9PAC/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Middle East respiratory syndrome-related coronavirus
• 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: 2.28 Å
• R-Value Free: 
  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural basis for pan-coronavirus inhibition of 3CL protease

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

(2026) Structure 

• 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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.1 kDa 
• Atom Count: 9,728 
• Modeled Residue Count: 1,208 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A [auth C], B [auth D], C [auth A], D [auth B]	306	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for K9N7C7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N7C7  Go to UniProtKB:  K9N7C7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CHF (Subject of Investigation/LOI)	E [auth C], F [auth A], G [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: 2.28 Å
• R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.047	α = 90
b = 94.865	β = 90
c = 152.236	γ = 90

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