3OYP

HCV NS3/4A in complex with ligand 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine.

Hagel, M.Niu, D.St.Martin, T.Sheets, M.P.Qiao, L.Bernard, H.Karp, R.M.Zhu, Z.Labenski, M.T.Chaturvedi, P.Nacht, M.Westlin, W.F.Petter, R.C.Singh, J.

(2011) Nat Chem Biol 7: 22-24

  • DOI: 10.1038/nchembio.492
  • Primary Citation of Related Structures:  
    3OYP

  • PubMed Abstract: 
  • Designing selective inhibitors of proteases has proven problematic, in part because pharmacophores that confer potency exploit the conserved catalytic apparatus. We developed a fundamentally different approach by designing irreversible inhibitors that target noncatalytic cysteines that are structurally unique to a target in a protein family ...

    Designing selective inhibitors of proteases has proven problematic, in part because pharmacophores that confer potency exploit the conserved catalytic apparatus. We developed a fundamentally different approach by designing irreversible inhibitors that target noncatalytic cysteines that are structurally unique to a target in a protein family. We have successfully applied this approach to the important therapeutic target HCV protease, which has broad implications for the design of other selective protease inhibitors.


    Organizational Affiliation

    Avila Therapeutics, Inc., Waltham, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease NS3A, B187Hepatitis C virus (isolate Japanese)Mutation(s): 2 
EC: 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.4.22 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 4AC, D16Hepatitis C virus (isolate Japanese)Mutation(s): 0 
EC: 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese))
Explore P26662 
Go to UniProtKB:  P26662
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidomimetic inhibitorE, F5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A], H [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0Y8
Query on 0Y8
E, FL-PEPTIDE LINKINGC14 H13 Br N2 O3PRO
Binding Affinity Annotations 
IDSourceBinding Affinity
3OY PDBBind:  3OYP IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.401α = 90
b = 94.401β = 90
c = 83.129γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2012-12-19
    Changes: Non-polymer description, Structure summary
  • Version 1.4: 2018-01-24
    Changes: Database references
  • Version 1.5: 2018-01-31
    Changes: Database references, Structure summary