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: 67.63 kDa 
• Atom Count: 5198 
• Residue Count: 601 
• Unique protein chains: 1

2OP9

Substrate Specificity Profiling and Identification of a New Class of Inhibitor for the Major Protease of the SARS Coronavirus

• DOI: 10.2210/pdb2OP9/pdb

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


• Deposited: 2007-01-27 Released: 2007-07-17 
• Deposition Author(s): Craik, C.S., Goetz, D.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Substrate Specificity Profiling and Identification of a New Class of Inhibitor for the Major Protease of the SARS Coronavirus.

Goetz, D.H., Choe, Y., Hansell, E., Chen, Y.T., McDowell, M., Jonsson, C.B., Roush, W.R., McKerrow, J., Craik, C.S.

(2007) Biochemistry 46: 8744-8752

• PubMed: 17605471 
• DOI: 10.1021/bi0621415
• Primary Citation of Related Structures:  
  2OP9


• PubMed Abstract: 
  

Severe acute respiratory syndrome (SARS) is an emerging infectious disease associated with a high rate of mortality. The SARS-associated coronavirus (SARS-CoV) has been identified as the etiological agent of the disease. Although public health procedures have been effective in combating the spread of SARS, concern remains about the possibility of a recurrence. Various approaches are being pursued for the development of efficacious therapeutics. One promising approach is to develop small molecule inhibitors of the essential major polyprotein processing protease 3Clpro. Here we report a complete description of the tetrapeptide substrate specificity of 3Clpro using fully degenerate peptide libraries consisting of all 160,000 possible naturally occurring tetrapeptides. The substrate specificity data show the expected P1-Gln P2-Leu specificity and elucidate a novel preference for P1-His containing substrates equal to the expected preference for P1-Gln. These data were then used to develop optimal substrates for a high-throughput screen of a 2000 compound small-molecule inhibitor library consisting of known cysteine protease inhibitor scaffolds. We also report the 1.8 A X-ray crystal structure of 3Clpro bound to an irreversible inhibitor. This inhibitor, an alpha,beta-epoxyketone, inhibits 3Clpro with a k3/Ki of 0.002 microM(-1) s(-1) in a mode consistent with the substrate specificity data. Finally, we report the successful rational improvement of this scaffold with second generation inhibitors. These data provide the foundation for a rational small-molecule inhibitor design effort based upon the inhibitor scaffold identified, the crystal structure of the complex, and a more complete understanding of P1-P4 substrate specificity.

---

Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab (pp1ab, ORF1AB) 3C-like proteinase (3CL-PRO, 3CLp)	A, B	302	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: 3Clpro, 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
WR1	A, B	NALPHA-[(BENZYLOXY)CARBONYL]-N-[(1R)-4-HYDROXY-1-METHYL-2-OXOBUTYL]-L-PHENYLALANINAMIDE C22 H26 N2 O5 UUOOAGBWJUGBMV-APWZRJJASA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
WR1	Ki :  2200   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.314	α = 90
b = 96.798	β = 103.2
c = 67.877	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-27 
• Released Date: 2007-07-17 
Deposition Author(s): Craik, C.S., Goetz, D.H.

Revision History 

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2008-01-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Experimental preparation