2OC8

Structure of Hepatitis C Viral NS3 protease domain complexed with NS4A peptide and ketoamide SCH503034


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key steps in structure-based optimization.

Prongay, A.J.Guo, Z.Yao, N.Pichardo, J.Fischmann, T.Strickland, C.Myers, J.Weber, P.C.Beyer, B.M.Ingram, R.Hong, Z.Prosise, W.W.Ramanathan, L.Taremi, S.S.Yarosh-Tomaine, T.Zhang, R.Senior, M.Yang, R.S.Malcolm, B.Arasappan, A.Bennett, F.Bogen, S.L.Chen, K.Jao, E.Liu, Y.T.Lovey, R.G.Saksena, A.K.Venkatraman, S.Girijavallabhan, V.Njoroge, F.G.Madison, V.

(2007) J.Med.Chem. 50: 2310-2318

  • DOI: 10.1021/jm060173k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of both the native holo-HCV NS3/4A protease domain and the protease domain with a serine 139 to alanine (S139A) mutation were solved to high resolution. Subsequently, structures were determined for a series of ketoamide inhibitors in c ...

    The structures of both the native holo-HCV NS3/4A protease domain and the protease domain with a serine 139 to alanine (S139A) mutation were solved to high resolution. Subsequently, structures were determined for a series of ketoamide inhibitors in complex with the protease. The changes in the inhibitor potency were correlated with changes in the buried surface area upon binding the inhibitor to the active site. The largest contribution to the binding energy arises from the hydrophobic interactions of the P1 and P2 groups as they bind to the S1 and S2 pockets [the numbering of the subsites is as defined in Berger, A.; Schechter, I. Philos. Trans. R. Soc. London, Ser. B 1970, 257, 249-264]. This correlation of the changes in potency with increased buried surface area contributed directly to the design of a potent tripeptide inhibitor of the HCV NS3/4A protease that is currently in clinical trials.


    Related Citations: 
    • Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide.
      Kim, J.L.,Morgenstern, K.A.,Lin, C.,Fox, T.,Dwyer, M.D.,Landro, J.A.,Chambers, S.P.,Markland, W.,Lepre, C.A.,O'Malley, E.T.,Harbeson, S.L.,Rice, C.M.,Murcko, M.A.,Caron, P.R.,Thomson, J.A.
      (1996) Cell 87: 343
    • Hepatitis C virus NS3-4A serine protease inhibitors: SAR of P'2 moiety with improved potency.
      Arasappan, A.,Njoroge, F.G.,Chan, T.Y.,Bennett, F.,Bogen, S.L.,Chen, K.,Gu, H.,Hong, L.,Jao, E.,Liu, Y.T.,Lovey, R.G.,Parekh, T.,Pike, R.E.,Pinto, P.,Santhanam, B.,Venkatraman, S.,Vaccaro, H.,Wang, H.,Yang, X.,Zhu, Z.,Mckittrick, B.,Saksena, A.K.,Girijavallabhan, V.,Pichardo, J.,Butkiewicz, N.,Ingram, R.,Malcolm, B.,Prongay, A.,Yao, N.,Marten, B.,Madison, V.,Kemp, S.,Levy, O.,Lim-Wilby, M.,Tamura, S.,Ganguly, A.K.
      (2005) Bioorg.Med.Chem.Lett. 15: 4180
    • Depeptidization efforts on P3-P2' alpha-ketoamide inhibitors of HCV NS3-4A serine protease: effect on HCV replicon activity.
      Bogen, S.L.,Ruan, S.,Liu, R.,Agrawal, S.,Pichardo, J.,Prongay, A.,Baroudy, B.,Saksena, A.K.,Girijavallabhan, V.,Njoroge, F.G.
      (2006) Bioorg.Med.Chem.Lett. 16: 1621
    • Hepatitis C virus NS3-4A serine protease inhibitors: use of a P2-P1 cyclopropyl alanine combination for improved potency.
      Bogen, S.,Saksena, A.K.,Arasappan, A.,Gu, H.,Njoroge, F.G.,Girijavallabhan, V.,Pichardo, J.,Butkiewicz, N.,Prongay, A.,Madison, V.
      (2005) Bioorg.Med.Chem.Lett. 15: 4515
    • Synthesis and biological activity of macrocyclic inhibitors of hepatitis C virus (HCV) NS3 protease.
      Chen, K.X.,Njoroge, F.G.,Prongay, A.,Pichardo, J.,Madison, V.,Girijavallabhan, V.
      (2005) Bioorg.Med.Chem.Lett. 15: 4475


    Organizational Affiliation

    Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA. andrew.prongay@spcorp.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hepatitis C virus
A, C
200Hepatitis C virus genotype 1a (isolate H)Mutation(s): 0 
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H))
Go to UniProtKB:  P27958
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hepatitis C virus
B, D
23Hepatitis C virus genotype 1a (isolate H)Mutation(s): 0 
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H))
Go to UniProtKB:  P27958
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HU5
Query on HU5

Download SDF File 
Download CCD File 
A
(1R,2S,5S)-N-[(1S)-3-AMINO-1-(CYCLOBUTYLMETHYL)-2,3-DIOXOPROPYL]-3-[(2S)-2-{[(TERT-BUTYLAMINO)CARBONYL]AMINO}-3,3-DIMETHYLBUTANOYL]-6,6-DIMETHYL-3-AZABICYCLO[3.1.0]HEXANE-2-CARBOXAMIDE
Ketoamide Inhibitor SCH503034, bound form
C27 H45 N5 O5
LHHCSNFAOIFYRV-ZYNAIFEFSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.192 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 223.871α = 90.00
b = 223.871β = 90.00
c = 74.962γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
SCALEPACKdata scaling
ADSCdata collection
X-PLORphasing
HKL-2000data reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-07-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance