4K8B

Crystal structure of HCV NS3/4A protease complexed with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Ligand bioactive conformation plays a critical role in the design of drugs that target the hepatitis C virus NS3 protease.

Laplante, S.R.Nar, H.Lemke, C.T.Jakalian, A.Aubry, N.Kawai, S.H.

(2014) J Med Chem 57: 1777-1789

  • DOI: 10.1021/jm401338c
  • Primary Citation of Related Structures:  
    4K8B

  • PubMed Abstract: 
  • A ligand-focused strategy employed NMR, X-ray, modeling, and medicinal chemistry to expose the critical role that bioactive conformation played in the design of a variety of drugs that target the HCV protease. The bioactive conformation (bound states) were determined for key inhibitors identified along our drug discovery pathway from the hit to clinical compounds ...

    A ligand-focused strategy employed NMR, X-ray, modeling, and medicinal chemistry to expose the critical role that bioactive conformation played in the design of a variety of drugs that target the HCV protease. The bioactive conformation (bound states) were determined for key inhibitors identified along our drug discovery pathway from the hit to clinical compounds. All adopt similar bioactive conformations for the common core derived from the hit peptide DDIVPC. A carefully designed SAR analysis, based on the advanced inhibitor 1 in which the P1 to P3 side chains and the N-terminal Boc were sequentially truncated, revealed a correlation between affinity and the relative predominance of the bioactive conformation in the free state. Interestingly, synergistic conformation effects on potency were also noted. Comparisons with clinical and recently marketed drugs from the pharmaceutical industry showed that all have the same core and similar bioactive conformations. This suggested that the variety of appendages discovered for these compounds also properly satisfy the bioactive conformation requirements and allowed for a large variety of HCV protease drug candidates to be designed.


    Organizational Affiliation

    Department of Chemistry, Boehringer-Ingelheim (Canada) Ltd., Research and Development , Laval, Québec H7S 2G5, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 proteaseA, B181Hepacivirus CMutation(s): 0 
EC: 3.4.21.98
UniProt
Find proteins for Q0ZNA6 (Hepacivirus C)
Explore Q0ZNA6 
Go to UniProtKB:  Q0ZNA6
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nonstructural proteinC, D12Hepacivirus CMutation(s): 0 
Gene Names: NS3-NS4
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 P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1RR (Subject of Investigation/LOI)
Query on 1RR

Download Ideal Coordinates CCD File 
F [auth A], J [auth B]N-(tert-butylcarbamoyl)-3-methyl-L-valyl-(4R)-N-[(1R,2S)-1-carboxy-2-ethenylcyclopropyl]-4-[(7-methoxy-2-phenylquinolin-4-yl)oxy]-L-prolinamide
C38 H47 N5 O7
YRUPMLSBJQBAAC-LSSONSMQSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], K [auth B], L [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], I [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.182α = 90
b = 76.182β = 90
c = 169.206γ = 120
Software Package:
Software NamePurpose
AMoREphasing
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2013-04-18 
  • Released Date: 2014-03-26 
  • Deposition Author(s): Nar, H.

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-26
    Type: Initial release