5MM6
 
 | | Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide | | Descriptor: | D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide, DIMETHYL SULFOXIDE, GLYCEROL, ... | | Authors: | Marca, A, Sandner, A, Heine, A, Klebe, G. | | Deposit date: | 2016-12-08 | | Release date: | 2017-12-20 | | Last modified: | 2018-06-27 | | Method: | X-RAY DIFFRACTION (1.29 Å) | | Cite: | Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide
to be published
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1MUE
 | | Thrombin-Hirugen-L405,426 | | Descriptor: | 2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDO-2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUOROPHENYL)METHYL]ACETAMIDE, HIRUDIN IIB, THROMBIN | | Authors: | Burgey, C.S, Robinson, K.A, Lyle, T.A, Nantermet, P.G, Selnick, H.G, Isaacs, R.C, 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, J.J, Yan, Y, Chen, Z, Kuo, L, Gardell, S.J, Shafer, J.A, Vacca, J.P. | | Deposit date: | 2002-09-23 | | Release date: | 2004-04-06 | | Last modified: | 2013-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Pharmacokinetic optimization of 3-amino-6-chloropyrazinone acetamide thrombin inhibitors. Implementation of P3 pyridine N-oxides to deliver an orally bioavailable series containing P1 N-benzylamides.
Bioorg.Med.Chem.Lett., 13, 2003
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1MU6
 | | Crystal Structure of Thrombin in Complex with L-378,622 | | Descriptor: | 2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUORO-6-PYRIDINYL)METHYL]ACETAMIDE, HIRUDIN IIB, THROMBIN | | Authors: | Burgey, C.S, Robinson, K.A, Lyle, T.A, Sanderson, P.E, Lewis, S.D, Lucas, B.J, Krueger, J.A, Singh, R, Miller-Stein, C, White, R.B, Wong, B, Lyle, E.A, Williams, P.D, Coburn, C.A, Dorsey, B.D, Barrow, J.C, Stranieri, M.T, Holahan, M.A, Sitko, G.R, Cook, J.J, McMasters, D.R, McDonough, C.M, Sanders, W.M, Wallace, A.A, Clayton, F.C, Bohn, D, Leonard, Y.M, Detwiler Jr, T.J, Lynch Jr, J.J, Yan, Y, Chen, Z, Kuo, L, Gardell, S.J, Shafer, J.A, Vacca, J.P.J. | | Deposit date: | 2002-09-23 | | Release date: | 2004-04-06 | | Last modified: | 2021-07-21 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines.
J.Med.Chem., 46, 2003
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5JZY
 | | Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 3-cyclohexyl-D-alanyl-N-[(4-carbamimidoylphenyl)methyl]-L-prolinamide, DIMETHYL SULFOXIDE, ... | | Authors: | Sandner, A, Heine, A, Klebe, G. | | Deposit date: | 2016-05-17 | | Release date: | 2017-06-07 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.27 Å) | | Cite: | Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
J.Med.Chem., 62, 2019
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5LPD
 | | Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(2-(aminomethyl)-5-chlorobenzyl) pyrrolidine-2-carboxamide | | Descriptor: | (2~{S})-~{N}-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2~{R})-2-azanyl-3-cyclohexyl-propanoyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | | Authors: | Sandner, A, Heine, A, Klebe, G. | | Deposit date: | 2016-08-12 | | Release date: | 2017-07-26 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
J.Med.Chem., 62, 2019
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5LCE
 | | Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(5-chloro-2-(hydroxymethyl)benzy l)pyrrolidine-2-carboxamide | | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-cyclohexyl-propanoyl]-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Sandner, A, Heine, A, Klebe, G. | | Deposit date: | 2016-06-21 | | Release date: | 2017-07-26 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.39 Å) | | Cite: | Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
J.Med.Chem., 62, 2019
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4LOY
 | | Crystal Structure Analysis of thrombin in complex with compound D57, 5-Chlorothiophene-2-carboxylic acid [(S)-2-[2-methyl-3-(2- oxopyrrolidin-1-yl)benzenesulfonylamino]-3-(4-methylpiperazin-1- yl)-3-oxopropyl]amide (SAR107375) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-Chloro-thiophene-2-carboxylic acid [(S)-2-[2-chloro-5-fluoro-3-(2-oxo-piperidin-1-yl)-benzenesulfonylamino]-3-(4-methyl-piperazin-1-yl)-3-oxo-propyl]-amide, Hirudin variant-2, ... | | Authors: | Stehlin-Gaon, C, Bocskei, Z. | | Deposit date: | 2013-07-14 | | Release date: | 2014-06-04 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | 5-Chlorothiophene-2-carboxylic acid [(S)-2-[2-methyl-3-(2-oxopyrrolidin-1-yl)benzenesulfonylamino]-3-(4-methylpiperazin-1-yl)-3-oxopropyl]amide (SAR107375), a selective and potent orally active dual thrombin and factor Xa inhibitor.
J.Med.Chem., 56, 2013
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4LXB
 | | Crystal Structure Analysis of thrombin in complex with compound D58 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-Chloro-thiophene-2-carboxylic acid [(S)-2-[2-difluoromethoxy-3-(2-oxo-piperidin-1-yl)-benzenesulfonylamino]-3-((S)-3-dimethylamino-pyrrolidin-1-yl)-3-oxo-propyl]-amide, Hirudin variant-1, ... | | Authors: | Stehlin-Gaon, C, Bocskei, Z. | | Deposit date: | 2013-07-29 | | Release date: | 2014-06-11 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.61 Å) | | Cite: | 5-Chlorothiophene-2-carboxylic acid [(S)-2-[2-methyl-3-(2-oxopyrrolidin-1-yl)benzenesulfonylamino]-3-(4-methylpiperazin-1-yl)-3-oxopropyl]amide (SAR107375), a selective and potent orally active dual thrombin and factor Xa inhibitor.
J.Med.Chem., 56, 2013
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4MLF
 | | Crystal structure for the complex of thrombin mutant D102N and hirudin | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, Hirudin variant-1, ... | | Authors: | Vogt, A.D, Pozzi, N, Chen, Z, Di Cera, E. | | Deposit date: | 2013-09-06 | | Release date: | 2013-09-25 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Essential role of conformational selection in ligand binding.
Biophys.Chem., 186C, 2014
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4YES
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3LDX
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2V3O
 | | Thrombin with 3-cycle with F | | Descriptor: | (2R)-[(4-CARBAMIMIDOYLPHENYL)AMINO]{3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYL-2-FLUOROPHENYL}ETHANOIC ACID, CALCIUM ION, HIRUDIN IIA, ... | | Authors: | Banner, D.W, Wessel, H.P. | | Deposit date: | 2007-06-19 | | Release date: | 2008-06-24 | | Last modified: | 2013-10-23 | | Method: | X-RAY DIFFRACTION (1.79 Å) | | Cite: | Fluorine in Pharmaceuticals: Looking Beyond Intuition.
Science, 317, 2007
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2V3H
 | | Thrombin with 3-cycle no F | | Descriptor: | (2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYLPHENYL}ACETIC ACID, CALCIUM ION, HIRUDIN IIA, ... | | Authors: | Banner, D.W, Obst, U. | | Deposit date: | 2007-06-18 | | Release date: | 2008-06-24 | | Last modified: | 2013-10-23 | | Method: | X-RAY DIFFRACTION (1.79 Å) | | Cite: | Fluorine in Pharmaceuticals: Looking Beyond Intuition.
Science, 317, 2007
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2UUF
 | | Thrombin-hirugen binary complex at 1.26A resolution | | Descriptor: | CALCIUM ION, HIRUDIN I, HUMAN ALPHA THROMBIN, ... | | Authors: | Ahmed, H.U, Blakeley, M.P, Cianci, M, Cruickshank, D.W.J, Hubbard, J.A, Helliwell, J.R. | | Deposit date: | 2007-03-02 | | Release date: | 2007-09-04 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.26 Å) | | Cite: | The Determination of Protonation States in Proteins.
Acta Crystallogr.,Sect.D, 63, 2007
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4HTC
 | | THE REFINED STRUCTURE OF THE HIRUDIN-THROMBIN COMPLEX | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, ALPHA-THROMBIN (LARGE SUBUNIT), ALPHA-THROMBIN (SMALL SUBUNIT), ... | | Authors: | Tulinsky, A, Rydel, T.J, Bode, W, Huber, R. | | Deposit date: | 1993-06-25 | | Release date: | 1994-01-31 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Refined structure of the hirudin-thrombin complex.
J.Mol.Biol., 221, 1991
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2UUK
 | | Thrombin-hirugen-gw420128 ternary complex at 1.39A resolution | | Descriptor: | CALCIUM ION, HIRUDIN I, HUMAN ALPHA THROMBIN, ... | | Authors: | Ahmed, H.U, Blakeley, M.P, Cianci, M, Cruickshank, D.W.J, Hubbard, J.A, Helliwell, J.R. | | Deposit date: | 2007-03-03 | | Release date: | 2007-09-04 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (1.39 Å) | | Cite: | The Determination of Protonation States in Proteins.
Acta Crystallogr.,Sect.D, 63, 2007
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2UUJ
 | | Thrombin-hirugen-gw473178 ternary complex at 1.32A resolution | | Descriptor: | CALCIUM ION, HIRUDIN I, HUMAN ALPHA THROMBIN, ... | | Authors: | Ahmed, H.U, Blakeley, M.P, Cianci, M, Cruickshank, D.W.J, Hubbard, J.A, Helliwell, J.R. | | Deposit date: | 2007-03-03 | | Release date: | 2007-09-04 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (1.32 Å) | | Cite: | The Determination of Protonation States in Proteins.
Acta Crystallogr.,Sect.D, 63, 2007
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5AHG
 | | Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine | | Descriptor: | ((4-Chlorophenyl)sulfamoyl))dimethylamine, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | | Authors: | Ruehmann, E, Heine, A, Klebe, G. | | Deposit date: | 2015-02-06 | | Release date: | 2015-08-26 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.24 Å) | | Cite: | Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
J.Med.Chem., 58, 2015
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5AF9
 | | Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-methoxy-N-(pyridin-2-yl)benzamide, ... | | Authors: | Ruehmann, E, Heine, A, Klebe, G. | | Deposit date: | 2015-01-20 | | Release date: | 2015-08-26 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.18 Å) | | Cite: | Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
J.Med.Chem., 58, 2015
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5AFZ
 | | Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-propyl)-3-phenyl-propanamide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Hirudin-2, N-(BENZYLSULFONYL)-D-PHENYLALANYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE, ... | | Authors: | Ruehmann, E, Heine, A, Klebe, G. | | Deposit date: | 2015-01-27 | | Release date: | 2015-08-26 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.53 Å) | | Cite: | Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
J.Med.Chem., 58, 2015
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5AFY
 | | Thrombin in complex with 3-chloro-benzamide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 3-CHLORO-BENZAMIDE, DIMETHYL SULFOXIDE, ... | | Authors: | Ruehmann, E, Heine, A, Klebe, G. | | Deposit date: | 2015-01-27 | | Release date: | 2015-08-26 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.12 Å) | | Cite: | Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
J.Med.Chem., 58, 2015
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2PKS
 | | Thrombin in complex with inhibitor | | Descriptor: | 4-({[4-(3-METHYLBENZOYL)PYRIDIN-2-YL]AMINO}METHYL)BENZENECARBOXIMIDAMIDE, Hirudin, SODIUM ION, ... | | Authors: | Xue, Y. | | Deposit date: | 2007-04-18 | | Release date: | 2008-04-22 | | Last modified: | 2017-10-18 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold.
Org.Biomol.Chem., 5, 2007
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5A2M
 | | Thrombin Inhibitor | | Descriptor: | (2S)-1-[(2R)-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]-N-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | | Authors: | Ruehmann, E, Heine, A, Klebe, G. | | Deposit date: | 2015-05-20 | | Release date: | 2016-06-01 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Thrombin Inhibition
To be Published
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3P17
 | | Thrombin Inhibition by Pyridin Derivatives | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-(pyridin-3-ylmethyl)-L-prolinamide, Hirudin variant-2, ... | | Authors: | Biela, A, Heine, A, Klebe, G. | | Deposit date: | 2010-09-30 | | Release date: | 2011-11-02 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.43 Å) | | Cite: | Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin.
J.Mol.Biol., 418, 2012
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3P70
 | | Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BENZAMIDINE, ... | | Authors: | Corral-Rodriguez, M.A, Bock, P.E, Hernandez-Carvajal, E, Gutierrez-Gallego, R, Fuentes-Prior, P. | | Deposit date: | 2010-10-11 | | Release date: | 2011-09-28 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Structural basis of thrombin-mediated factor V activation: the Glu666-Glu672 sequence is critical for processing at the heavy chain-B domain junction.
Blood, 117, 2011
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