7JT7

Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4

• PDB DOI: https://doi.org/10.2210/pdb7JT7/pdb

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


• Deposited: 2020-08-17 Released: 2021-03-17 
• Deposition Author(s): Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.225 
• R-Value Work: 0.174 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors.

Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

(2021) Nat Commun 12: 2016-2016

• PubMed: 33795671 
• DOI: https://doi.org/10.1038/s41467-021-22362-2
• Primary Citation of Related Structures:  
  7JST, 7JSU, 7JT0, 7JT7, 7JW8


• PubMed Abstract: 
  

  We report the identification of three structurally diverse compounds - compound 4, GC376, and MAC-5576 - as inhibitors of the SARS-CoV-2 3CL protease. Structures of each of these compounds in complex with the protease revealed strategies for further development, as well as general principles for designing SARS-CoV-2 3CL protease inhibitors. These compounds may therefore serve as leads for the basis of building effective SARS-CoV-2 3CL protease inhibitors.

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Organizational Affiliation: 

Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, USA.

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: 34.46 kDa 
• Atom Count: 2,677 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	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
TG3 (Subject of Investigation/LOI)	B [auth A]	ethyl (4R)-4-[[(2S)-4-methyl-2-[[(2S,3R)-3-[(2-methylpropan-2-yl)oxy]-2-(phenylmethoxycarbonylamino)butanoyl]amino]pentanoyl]amino]-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pentanoate C33 H52 N4 O8 GENYQFMDDNZIRG-UCWBBBRQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.225 
• R-Value Work: 0.174 
• R-Value Observed: 0.179 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.215	α = 90
b = 81.945	β = 117.11
c = 54.187	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 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2021-04-14
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description