Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 47.42 kDa 
• Atom Count: 2,881 
• Modelled Residue Count: 369 
• Deposited Residue Count: 446 
• Unique protein chains: 2

 2OBQ

Discovery of the HCV NS3/4A Protease Inhibitor SCH503034. Key Steps in Structure-Based Optimization

• PDB DOI: 10.2210/pdb2OBQ/pdb

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


• Deposited: 2006-12-19 Released: 2007-07-31 
• Deposition Author(s): Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers Jr., J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R., Arasappan, A., Bennett, F., Bogen, S.F., Chen, K., Jao, E., Liu, Y., Love, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.264 
• R-Value Work: 0.203 

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 Jr., 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

• PubMed: 17444623 
• DOI: 10.1021/jm060173k
• Primary Citation of Related Structures:  
  2O8M, 2OBO, 2OBQ, 2OC0, 2OC1, 2OC7, 2OC8


• 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 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.

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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.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

• 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

• 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

• 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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatitis C virus	A, C	200	Hepacivirus C	Mutation(s): 0  Gene Names: HCV 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 P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958  Go to UniProtKB:  P27958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatitis C virus	B, D	23	N/A	Mutation(s): 0
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958  Go to UniProtKB:  P27958

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.264 
• R-Value Work: 0.203 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.57	α = 90
b = 225.57	β = 90
c = 75.72	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-31 
Deposition Author(s): Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers Jr., J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R., Arasappan, A., Bennett, F., Bogen, S.F., Chen, K., Jao, E., Liu, Y., Love, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.

Revision History  

• Version 1.0: 2007-07-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2012-02-22
  Changes: Structure summary
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations