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To find amine replacements in 5, commercial databases were searched for small primary amines using a flexible 3D pharmacophore search. The query based on the extrapolated binding mode of 5 comprises the following features: 4 (5) spheres fixing the location of the primary amine and the center of a phenyl ring (or alternatively an aromatic 5/6 condensed bicycle of ANY atoms) as well as a spatial plane through the ring. The resulting hits were attached to the diphenylalanine proline scaffold. 5-Chlorobenzothiophene was selected based on minimization of these structures in the active site of thrombin. In the course of our work, similar findings for FXa inhibitors were reported: Coi-Sledeski, Y.M.; Kearney, R.; Poli, G.; Pauls, H.; Gardner, C.; Gong, Y.; Becker, M.; Davis, R.; Spada, A.; Liang, G.; Chu, V.; Brown, K.; Collussi, D.; Leadley, Jr., R.; Rebello, S.; Moxey, P.; Morgan, S.; Bentley, R.; Kasiewski, C.; Maignan, S.; Guilloteau, J.-P.; Mikol, V. J. Med. Chem. 2003, 46, 681-684;
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0037424704
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Christopher S.; Burgey, C.S.; Robinson, K.A.; Lyle, T.A.; Nantermet, P.G.; Selnick, H.G.; Isaacs, R.C.A.; Lewis, S.D.; Lucas, B.J.; Krueger, J.A.; Singh, R.; Miller-Stein, C.; White, R.B.; Wong, B.; Lyle, E.A.; Stranieri, M.T.; Cook, J.J.; McMasters, D.R.; Pellicore, J.M.; Pal, S.; Wallace, A.A.; Clayton, F.C.; Bohn, D.; Welsh, D.C.; Lynch, Jr., J.J.; Yan, Y.; Chen, Z.; Kuo, L.; Gardell, S.J.; Shafer, J.A.; Vacca, J.P. Bioorg. Med. Chem Lett. 2003, 13, 1353-1357.
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0037434510
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33745630274
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note
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The resolution of the final structures were 3.2 Å (7), 1.8 Å for (8) and 2.8 Å (9). The structures are deposited in the PDB with the respective codes 2BVX (7), 2BXT (8) and 2BXU (9).
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2542523899
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Young, M.B.; Barrow, J.C.; Glass, K.L.; Lundell, G.F.; Newton, C.L.; Pellicore, J.M.; Rittle, K.E.; Selnick, H.G.; Stauffer, K.J.; Vacca, J.P.; Williams, P.D.; Bohn, D.; Clayton, F.C.; Cook, J.J.; Krueger, J.A.; Kuo, L.C.; Lewis, S.D.; Lucas, B.J.; McMasters, D.R.; Miller-Stein, C.; Pietrak, B.L.; Wallace, A.A.; White, R.B.; Wong, B.; Yan, Y.; Nantermet, P. G. J. Med. Chem. 2004, 47, 2995-3008.
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Young, M.B.1
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Glass, K.L.3
Lundell, G.F.4
Newton, C.L.5
Pellicore, J.M.6
Rittle, K.E.7
Selnick, H.G.8
Stauffer, K.J.9
Vacca, J.P.10
Williams, P.D.11
Bohn, D.12
Clayton, F.C.13
Cook, J.J.14
Krueger, J.A.15
Kuo, L.C.16
Lewis, S.D.17
Lucas, B.J.18
McMasters, D.R.19
Miller-Stein, C.20
Pietrak, B.L.21
Wallace, A.A.22
White, R.B.23
Wong, B.24
Yan, Y.25
Nantermet, P.G.26
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