7TIA | pdb_00007tia

Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-14

• PDB DOI: https://doi.org/10.2210/pdb7TIA/pdb

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


• Deposited: 2022-01-13 Released: 2022-05-04 
• Deposition Author(s): Forouhar, F., Liu, H., Iketani, S., Zack, A., Khanizeman, N., Bednarova, E., Fowler, B., Hong, S.J., Mohri, H., Nair, M.S., Huang, Y., Tay, N.E.S., Lee, S., Karan, C., Resnick, S.J., Quinn, C., Li, W., Shion, H., Jurtschenko, C., Lauber, M.A., McDonald, T., Stokes, M.E., Hurst, B., Rovis, T., Chavez, A., Ho, D.D., Stockwell, B.R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19.

Liu, H., Iketani, S., Zask, A., Khanizeman, N., Bednarova, E., Forouhar, F., Fowler, B., Hong, S.J., Mohri, H., Nair, M.S., Huang, Y., Tay, N.E.S., Lee, S., Karan, C., Resnick, S.J., Quinn, C., Li, W., Shion, H., Xia, X., Daniels, J.D., Bartolo-Cruz, M., Farina, M., Rajbhandari, P., Jurtschenko, C., Lauber, M.A., McDonald, T., Stokes, M.E., Hurst, B.L., Rovis, T., Chavez, A., Ho, D.D., Stockwell, B.R.

(2022) Nat Commun 13: 1891-1891

• PubMed: 35393402 
• DOI: https://doi.org/10.1038/s41467-022-29413-2
• Primary Citation Related Structures: 
  7TIA, 7TIU, 7TIV, 7TIW, 7TIX, 7TIY, 7TIZ, 7TJ0


• PubMed Abstract: 
  

  The SARS-CoV-2 3CL protease is a critical drug target for small molecule COVID-19 therapy, given its likely druggability and essentiality in the viral maturation and replication cycle. Based on the conservation of 3CL protease substrate binding pockets across coronaviruses and using screening, we identified four structurally distinct lead compounds that inhibit SARS-CoV-2 3CL protease. After evaluation of their binding specificity, cellular antiviral potency, metabolic stability, and water solubility, we prioritized the GC376 scaffold as being optimal for optimization. We identified multiple drug-like compounds with <10 nM potency for inhibiting SARS-CoV-2 3CL and the ability to block SARS-CoV-2 replication in human cells, obtained co-crystal structures of the 3CL protease in complex with these compounds, and determined that they have pan-coronavirus activity. We selected one compound, termed coronastat, as an optimized lead and characterized it in pharmacokinetic and safety studies in vivo. Coronastat represents a new candidate for a small molecule protease inhibitor for the treatment of SARS-CoV-2 infection for eliminating pandemics involving coronaviruses.

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Organizational Affiliation: 
• Department of Chemistry, Columbia University, New York, NY, 10027, USA.
Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Sulzberger Columbia Genome Center, Columbia University, New York, NY, 10032, USA.
Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Waters Corporation, 34 Maple Street, Milford, MA, 01757, USA.
Department of Pharmacology and Molecular Therapeutics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil.
Institute for Antiviral Research, Utah State University, Logan, UT, 84322, USA.
Department of Chemistry, Columbia University, New York, NY, 10027, USA. [e-mail].
Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA. [e-mail].
Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA. [e-mail].
Department of Chemistry, Columbia University, New York, NY, 10027, USA. [e-mail].
Department of Biological Sciences, Columbia University, New York, NY, 10027, USA. [e-mail].

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: 34.29 kDa 
• Atom Count: 2,542 
• Modeled Residue Count: 303 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XTP (Subject of Investigation/LOI)	B [auth A]	benzyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate C21 H29 N3 O5 PJKBYKVMAKWNAK-BZSNNMDCSA-N
SCN	C [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.551	α = 90
b = 81.778	β = 114.61
c = 51.876	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Forouhar, F., Liu, H., Iketani, S., Zack, A., Khanizeman, N., Bednarova, E., Fowler, B., Hong, S.J., Mohri, H., Nair, M.S., Huang, Y., Tay, N.E.S., Lee, S., Karan, C., Resnick, S.J., Quinn, C., Li, W., Shion, H., Jurtschenko, C., Lauber, M.A., McDonald, T., Stokes, M.E., Hurst, B., Rovis, T., Chavez, A., Ho, D.D., Stockwell, B.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Structure summary
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary