Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.91 kDa 
• Atom Count: 2932 
• Modelled Residue Count: 373 
• Deposited Residue Count: 444 
• Unique protein chains: 2

2GVF

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

• PDB DOI: 10.2210/pdb2GVF/pdb

• Classification: HYDROLASE
• Organism(s): Hepacivirus C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-02 Released: 2007-01-23 
• Deposition Author(s): 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.

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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 

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

• PubMed: 16730985 
• 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.

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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

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Organizational Affiliation: 

Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
polyprotein	A, C	199	Hepacivirus C	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 P26664 (Hepatitis C virus genotype 1a (isolate 1)) Explore P26664  Go to UniProtKB:  P26664

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	B, D	23	N/A	Mutation(s): 0
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1)) Explore P26664  Go to UniProtKB:  P26664

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHN	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
ZN	E [auth A], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 224.615	α = 90
b = 224.615	β = 90
c = 75.321	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
DENZO	data reduction
X-PLOR	model building
X-PLOR	refinement
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-02 
• Released Date: 2007-01-23 
Deposition Author(s): 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.

Revision History  

• 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