Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2576 
• Residue Count: 302 
• Unique protein chains: 1

2ALV

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

• DOI: 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 

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: 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]

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  Gene Names: rep, 1a-1b EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (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	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CY6	IC50:  70000   nM  BindingDB
CY6	IC50 :  70000   nM  PDBBind
CY6	IC50:  800000   nM  BindingDB

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

• Deposited Date: 2005-08-08 
• 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