3E9S | pdb_00003e9s

A new class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

• PDB DOI: https://doi.org/10.2210/pdb3E9S/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-23 Released: 2008-10-07 
• Deposition Author(s): Mesecar, A.D., Ratia, K., Pegan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.192 (DCC) 

Literature

A new class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

Mesecar, A.D., Ratia, K., Pegan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.17 kDa 
• Atom Count: 2,614 
• Modeled Residue Count: 317 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A	318	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: 1a EC: 3.4.22
UniProt
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus) Explore P0C6U8  Go to UniProtKB:  P0C6U8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTT	B [auth A]	5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide C20 H20 N2 O UVERBUNNCOKGNZ-CQSZACIVSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.192 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.703	α = 90
b = 90.684	β = 90
c = 109.537	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Mesecar, A.D., Ratia, K., Pegan, S.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary