8UDJ

Crystal structure of SARS-CoV-2 3CL protease with inhibitor DEL_2

• PDB DOI: https://doi.org/10.2210/pdb8UDJ/pdb

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


• Deposited: 2023-09-28 Released: 2024-12-25 
• Deposition Author(s): Forouhar, F., Liu, H., Zack, A., Iketani, S., Williams, A., Vaz, D.R., Habashi, D.L., Resnick, S.J., 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: 1.85 Å
• R-Value Free: 0.203 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening

Liu, H., Zack, A., Forouhar, F., Iketani, S., Williams, A., Vaz, D.R., Habashi, D.L., Choi, K., Resnick, S.J., Chavez, A., Ho, D.D., Stockwell, B.R.

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)

Macromolecule Content

• Total Structure Weight: 34.41 kDa 
• Atom Count: 2,528 
• Modelled Residue Count: 302 
• 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  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
WB5 (Subject of Investigation/LOI)	B [auth A]	2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-(methylamino)-4-oxo-1-phenylbutan-2-yl]-D-phenylalaninamide C30 H31 Cl2 N5 O3 PQNNKOZAACJZJY-WYMJOSIYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.203 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.626	α = 90
b = 81.922	β = 117.42
c = 54.594	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Forouhar, F., Liu, H., Zack, A., Iketani, S., Williams, A., Vaz, D.R., Habashi, D.L., Resnick, S.J., Chavez, A., Ho, D.D., Stockwell, B.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release