2ZU3

Complex structure of CVB3 3C protease with TG-0204998


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Inhibition Specificities of 3C and 3C-like Proteases by Zinc-coordinating and Peptidomimetic Compounds

Lee, C.C.Kuo, C.J.Ko, T.P.Hsu, M.F.Tsui, Y.C.Chang, S.C.Yang, S.Chen, S.J.Chen, H.C.Hsu, M.C.Shih, S.R.Liang, P.H.Wang, A.H.-J.

(2009) J.Biol.Chem. 284: 7646-7655

  • DOI: 10.1074/jbc.M807947200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human coxsackievirus (CV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. In picornavirus, a chymotrypsin-like protease (3C(pro)) is required for viral replication by processing the polyproteins, and thus it ...

    Human coxsackievirus (CV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. In picornavirus, a chymotrypsin-like protease (3C(pro)) is required for viral replication by processing the polyproteins, and thus it is regarded as an antiviral drug target. A 3C-like protease (3CL(pro)) also exists in human coronaviruses (CoV) such as 229E and the one causing severe acute respiratory syndrome (SARS). To combat SARS, we previously had developed peptidomimetic and zinc-coordinating inhibitors of 3CL(pro). As shown in the present study, some of these compounds were also found to be active against 3C(pro) of CV strain B3 (CVB3). Several crystal structures of 3C(pro) from CVB3 and 3CL(pro) from CoV-229E and SARS-CoV in complex with the inhibitors were solved. The zinc-coordinating inhibitor is tetrahedrally coordinated to the His(40)-Cys(147) catalytic dyad of CVB3 3C(pro). The presence of specific binding pockets for the residues of peptidomimetic inhibitors explains the binding specificity. Our results provide a structural basis for inhibitor optimization and development of potential drugs for antiviral therapies.


    Organizational Affiliation

    Structural Biology Program, Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3C proteinase
A
183Coxsackievirus B3 (strain Nancy)Mutation(s): 0 
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Go to UniProtKB:  P03313
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZU3
Query on ZU3

Download SDF File 
Download CCD File 
A
N-[(benzyloxy)carbonyl]-3-[(2,2-dimethylpropanoyl)amino]-L-alanyl-N-[(1R)-4-oxo-1-{[(3S)-2-oxopyrrolidin-3-yl]methyl}pentyl]-L-leucinamide
TG-0204998
C32 H49 N5 O7
IEQRDAZPCPYZAJ-QYOOZWMWSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000568 (ZU3)
Query on PRD_000568
ATG-0204998Peptide-like / Enzyme inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZU3Ki: 800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.800α = 90.00
b = 64.620β = 115.92
c = 39.520γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
HKL-2000data collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Type: Structure summary
  • Version 1.3: 2014-04-16
    Type: Refinement description