11RO | pdb_000011ro

Crystal Structure of SARS-CoV-2 Mpro with UM-005

• PDB DOI: https://doi.org/10.2210/pdb11RO/pdb

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


• Deposited: 2026-03-10 Released: 2026-04-22 
• Deposition Author(s): Shaqra, A.M., Adnan, S.F.Z., Lee, L.T., Iyer, V., Jung, K., Intravaia, L.E., Kaur, J., Schiffer, C.A.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.239 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Nitrile-Based Inhibitors Targeting both SARS-CoV‐2 Main Protease and Human Cathepsin L.

Barasa, L., Chen, Y., Shaqra, A.M., Adnan, S.F.Z., Intravaia, L.E., Huchaiah, S., Allabaji, A., S, K.K., Vidadala, S.R., Patil, S.N., Hale, J., Schiffer, C.A., Fitzgerald, K.A., Thompson, P.R.

(2026) ACS Med Chem Lett 17: 1956-1965

• PubMed: 42741323 
• DOI: https://doi.org/10.1021/acsmedchemlett.6c00236
• Primary Citation Related Structures: 
  11RO, 12AF


• PubMed Abstract: 
  

  The SARS-CoV-2 main protease (M ^pro ) and host cysteine protease cathepsin L (CatL) are both attractive targets for antiviral intervention. Herein we describe the rational design and synthesis of dual M ^pro /CatL inhibitors derived from the previously reported leads SM141 and SM142 . Optimization focused on replacement of the acrylate ester warhead in SM141 and SM142 with a nitrile, modifying the P2, P3, and P4 capping groups, and variation of the P1 lactam ring size. In addition, conformational restriction was achieved through macrocyclization between the P1 and P4 side chains to enhance binding affinity. These efforts identified multiple dual-target inhibitors with nanomolar potency against both M ^pro and CatL and potent antiviral activity as well as selective M ^pro inhibitors with strong enzymatic activity. Targeting both a viral protease and a host factor may provide more durable antiviral efficacy by reducing susceptibility to resistance arising from viral evolution of M ^pro .

---

Organizational Affiliation: 
• Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States.
Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States.
Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States.
Syngene International Ltd., Bommasandra-Jigani Link Road, Biocon Park, Bangalore 560100 India.
Hale MedChem Advisors LLC, 233 Hazel Avenue, Westfield, New Jersey 07090, United States.

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: 68.2 kDa 
• Atom Count: 5,012 
• Modeled Residue Count: 610 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1DAK (Subject of Investigation/LOI)	C [auth A]	N-(trifluoroacetyl)-D-phenylalanyl-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-phenylalaninamide C27 H30 F3 N5 O4 YYCJAYZMYBJOBU-LWULPBRVSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002602 (A1DAK)	C [auth A]	N-(trifluoroacetyl)-D-phenylalanyl-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-phenylalaninamide	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.239 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.671	α = 115.81
b = 54.175	β = 99.97
c = 62.213	γ = 90.08

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
XDS	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Shaqra, A.M., Adnan, S.F.Z., Lee, L.T., Iyer, V., Jung, K., Intravaia, L.E., Kaur, J., Schiffer, C.A.

---

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release
  
• Version 1.1: 2026-10-07
  Changes: Database references