2GVF

HCV NS3-4A protease domain complexed with a macrocyclic ketoamide inhibitor, SCH419021


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

P2-P4 macrocyclic inhibitors of hepatitis C virus NS3-4A serine protease.

Arasappan, A.Njoroge, F.G.Chen, K.X.Venkatraman, S.Parekh, T.N.Gu, H.Pichardo, J.Butkiewicz, N.Prongay, A.Madison, V.Girijavallabhan, V.

(2006) Bioorg Med Chem Lett 16: 3960-3965

  • DOI: 10.1016/j.bmcl.2006.05.022
  • Primary Citation of Related Structures:  
    2GVF

  • PubMed Abstract: 
  • Synthesis and HCV NS3 serine protease inhibitory activity of 4-hydroxyproline derived macrocyclic inhibitors and SAR around this macrocyclic core is described in this communication. X-ray structure of inhibitor 38 bound to the protease is discussed.


    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., Landro, J.A., Chambers, S.P., Markland, W., Lepre, C., O'Malley, E.
      (1996) Cell 87: 343
    • Mutations conferring resistance to SCH6, a novel hepatitis C virus NS3/4A protease inhibitor. Reduced RNA replication fitness and partial rescue by second-site mutations
      Yi, M., Tong, X., Skelton, A., Chase, R., Chen, T., Prongay, A., Bogen, S.L., Saksena, A.K., Njoroge, F.G., Veselenak, R.L., Pyles, R.B., Bourne, N., Malcolm, B.A., Lemon, S.M.
      (2006) J Biol Chem 281: 8205
    • Hepatitis C NS3 protease inhibition by peptidyl-alpha-ketoamide inhibitors: kinetic mechanism and structure
      Liu, Y., Stoll, V.S., Richardson, P.L., Saldivar, A., Klaus, J.L., Molla, A., Kohlbrenner, W., Kati, W.M.
      (2004) Arch Biochem Biophys 421: 207
    • 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.J., 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

    Organizational Affiliation

    Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. ashok.arasappan@spcorp.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
polyproteinA, C199Hepacivirus CMutation(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 P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinB, D23N/AMutation(s): 0 
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHN (Subject of Investigation/LOI)
Query on NHN

Download Ideal Coordinates CCD File 
F [auth A](6R,8S,11S)-11-CYCLOHEXYL-N-(1-{[(2-{[(1S)-2-(DIMETHYLAMINO)-2-OXO-1-PHENYLETHYL]AMINO}-2-OXOETHYL)AMINO](OXO)ACETYL}BUTYL)-10,13-DIOXO-2,5-DIOXA-9,12-DIAZATRICYCLO[14.3.1.1~6,9~]HENICOSA-1(20),16,18-TRIENE-8-CARBOXAMIDE
C42 H56 N6 O9
RJPSYFVTRHPRGV-HVHRWFTHSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], G [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NHN PDBBind:  2GVF Ki: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.615α = 90
b = 224.615β = 90
c = 75.321γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance