2K1Q

NMR structure of hepatitis c virus ns3 serine protease complexed with the non-covalently bound phenethylamide inhibitor


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Binding of a noncovalent inhibitor exploiting the S' region stabilizes the hepatitis C virus NS3 protease conformation in the absence of cofactor.

Gallo, M.Pennestri, M.Bottomley, M.J.Barbato, G.Eliseo, T.Paci, M.Narjes, F.De Francesco, R.Summa, V.Koch, U.Bazzo, R.Cicero, D.O.

(2009) J.Mol.Biol. 385: 1142-1155

  • DOI: 10.1016/j.jmb.2008.11.017

  • PubMed Abstract: 
  • We present the first structure of a noncovalent inhibitor bound to the protease domain of hepatitis C virus NS3 protein (NS3p), solved by NMR. The inhibitor exploits interactions with the S' region of NS3p to form a long-lived complex, although the a ...

    We present the first structure of a noncovalent inhibitor bound to the protease domain of hepatitis C virus NS3 protein (NS3p), solved by NMR. The inhibitor exploits interactions with the S' region of NS3p to form a long-lived complex, although the absence of negative charges strongly reduces the association rate. The inhibitor stabilizes the N-terminal domain of NS3p and the substrate-binding site, and correctly aligns catalytic His-Asp residues. These actions were previously attributed exclusively to the cofactor NS4A, which interacts with the N-terminal domain of the NS3p and functions as an activator in vivo. The structure of the inhibitor/NS3p complex is very similar to that of the NS3p-NS4A complex, showing that binding of the NS4A cofactor is not the only event leading to a stable active-site conformation.


    Organizational Affiliation

    Department of Chemical Science and Technology, Università di Roma Tor Vergata Via della Ricerca Scientifica 1, 00133 Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS3 PROTEASE
A
186Hepacivirus CMutation(s): 0 
Find proteins for P90191 (Hepacivirus C)
Go to UniProtKB:  P90191
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHENETHYLAMIDE
B
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FE3
Query on FE3
B
NON-POLYMERC9 H10 Cl N O2

--

IBU
Query on IBU
B
NON-POLYMERC5 H10 O3

--

OBF
Query on OBF
B
L-peptide linkingC4 H7 F2 N O2

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2K1Q Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance