ISDA

Deposition Date 2006-12-19

Release Date 2007-07-31

Last Version Date 2023-08-30

Entry Detail

PDB ID:

2OBO

Keywords:

HYDROLASE/HYDROLASE INHIBITOR

Title:

Structure of HEPATITIS C VIRAL NS3 protease domain complexed with NS4A peptide and ketoamide SCH476776

Biological Source:

Source Organism:

Hepatitis C virus (Taxon ID: 11103)
Hepatitis C virus (Taxon ID: 31647)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.60 Å

R-Value Free:

0.29

R-Value Work:

0.17

Space Group:

H 3 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HCV NS3 protease
Chain IDs:A, C
Chain Length:200
Number of Molecules:2
Biological Source:Hepatitis C virus

UniProt ID:Q91RS4 Pfam ID:PF02907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HCV NS4A peptide
Mutations:C22S
Chain IDs:B, D
Chain Length:23
Number of Molecules:2
Biological Source:Hepatitis C virus

UniProt ID:Q9QP06 Pfam ID:PF01006

Ligand Molecules

BME

HUD

Peptide-like Molecules

PRD_000958

Primary Citation

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, 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, 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, Chen, K.X, Njoroge, F.G, Prongay, A, Pichardo, J, Madison, V, Girijavallabhan, V, Bogen, S, Saksena, A.K, Arasappan, A, Gu, H, Njoroge, F.G, Girijavallabhan, V, Pichardo, J, Butkiewicz, N, Prongay, A, Madison, V, 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.Show

J.Med.Chem. 50 2310 2318 (2007)

PMID: 17444623 DOI: 10.1021/jm060173k

Abstact

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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