7C8R | pdb_00007c8r

Complex Structure of SARS-CoV-2 3CL Protease with TG-0203770

• PDB DOI: https://doi.org/10.2210/pdb7C8R/pdb

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


• Deposited: 2020-06-03 Released: 2020-06-17 
• Deposition Author(s): Lee, C.C., Wang, A.H.J., Kuo, C.J., Liang, P.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.205 (DCC) 

Starting Model: experimental

Literature

Complex Structures and Cellular Activities of the Potent SARS-CoV-2 3CLpro Inhibitors Guiding Drug Discovery Against COVID-19

Kuo, C.J., Shie, J.J., Lin, C.H., Lin, Y.L., Hsieh, M.C., Lee, C.C., Chang, S.Y., Wang, A.H.J., Liang, P.H.

To be published.

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: 2,458 
• Modeled Residue Count: 301 
• 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  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: 2.30 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.205 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.39	α = 90
b = 104.39	β = 90
c = 90.233	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Lee, C.C., Wang, A.H.J., Kuo, C.J., Liang, P.H.

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 2.0: 2021-01-20
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2021-03-10
  Changes: Structure summary
• Version 2.2: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.3: 2024-10-16
  Changes: Structure summary