2QIQ | pdb_00002qiq

Structure-based Design and Synthesis and Biological Evaluation of Peptidomimetic SARS-3CLpro Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2QIQ/pdb

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


• Deposited: 2007-07-05 Released: 2008-02-12 
• Deposition Author(s): Grum-Tokars, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.275 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Structure-based design, synthesis, and biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors.

Ghosh, A.K., Xi, K., Grum-Tokars, V., Xu, X., Ratia, K., Fu, W., Houser, K.V., Baker, S.C., Johnson, M.E., Mesecar, A.D.

(2007) Bioorg Med Chem Lett 17: 5876-5880

• PubMed: 17855091 
• DOI: https://doi.org/10.1016/j.bmcl.2007.08.031
• Primary Citation Related Structures: 
  2QIQ


• PubMed Abstract: 
  

  Structure-based design, synthesis, and biological evaluation of a series of peptidomimetic severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors are described. These inhibitors were designed and synthesized based upon our X-ray crystal structure of inhibitor 1 bound to SARS-CoV 3CLpro. Incorporation of Boc-Ser as the P(4)-ligand resulted in enhanced SARS-CoV 3CLpro inhibitory activity. Structural analysis of the inhibitor-bound X-ray structure revealed high binding affinity toward the enzyme.

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Organizational Affiliation: 
• Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, 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.

Macromolecule Content 

• Total Structure Weight: 33.97 kDa 
• Atom Count: 2,538 
• Modeled Residue Count: 301 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	301	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: rep
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYV	B [auth A]	ETHYL (4R)-4-{[(2R,5S)-5-{[N-(TERT-BUTOXYCARBONYL)-L-SERYL]AMINO}-6-METHYL-2-(3-METHYLBUT-2-EN-1-YL)-4-OXOHEPTANOYL]AMINO}-5-[(3R)-2-OXOPYRROLIDIN-3-YL]PENTANOATE C32 H54 N4 O9 CSVHTXSZRNRRSB-AHPXAKOISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.275 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.325	α = 90
b = 82.225	β = 104.67
c = 53.684	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Grum-Tokars, V.

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description