2ALV

X-ray structural analysis of SARS coronavirus 3CL proteinase in complex with designed anti-viral inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2ALV/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-08-08 Released: 2006-08-08 
• Deposition Author(s): Ghosh, A.K., Xi, K., Ratia, K., Santarsiero, B.D., Fu, W., Harcourt, B.H., Rota, P.A., Baker, S.C., Johnson, M.E., Mesecar, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.315 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 

Starting Model: experimental

Literature

Design and synthesis of peptidomimetic severe acute respiratory syndrome chymotrypsin-like protease inhibitors.

Ghosh, A.K., Xi, K., Ratia, K., Santarsiero, B.D., Fu, W., Harcourt, B.H., Rota, P.A., Baker, S.C., Johnson, M.E., Mesecar, A.D.

(2005) J Med Chem 48: 6767-6771

• PubMed: 16250632 
• DOI: https://doi.org/10.1021/jm050548m
• Primary Citation of Related Structures:  
  2ALV


• PubMed Abstract: 
  

  Design, synthesis, and biological evaluation of peptidomimetic severe acute respiratory syndrome chymotrypsin-like protease (SARS-3CLpro) inhibitors for severe acute respiratory syndrome coronavirus (SARS-CoV) are described. These inhibitors exhibited antiviral activity against SARS-CoV in infected cells in the micromolar range. An X-ray crystal structure of our lead inhibitor (4) bound to SARS-3CLpro provided important drug-design templates for the design of small-molecule inhibitors.

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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: 34.36 kDa 
• Atom Count: 2,576 
• Modelled Residue Count: 302 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  EC: 3.4.22
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
CY6	B [auth A]	N-((3S,6R)-6-((S,E)-4-ETHOXYCARBONYL-1-((S)-2-OXOPYRROLIDIN-3-YL)BUT-3-EN-2-YLCARBAMOYL)-2,9-DIMETHYL-4-OXODEC-8-EN-3-YL)-5-METHYLISOXAZOLE-3-CARBOXAMIDE C29 H42 N4 O7 CSNQHKJCKPMZCY-YFUAOJPXSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CY6	PDBBind:  2ALV	IC50: 7.00e+4 (nM) from 1 assay(s)
	BindingDB:  2ALV	IC50: 7.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.315 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.098	α = 90
b = 83.24	β = 104.409
c = 53.696	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Ghosh, A.K., Xi, K., Ratia, K., Santarsiero, B.D., Fu, W., Harcourt, B.H., Rota, P.A., Baker, S.C., Johnson, M.E., Mesecar, A.D.

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.4: 2023-08-23
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary