2ZF0
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![BU of 2zf0 by Molmil](/molmil-images/mine/2zf0) | Exploring Thrombin S1 Pocket | Descriptor: | D-phenylalanyl-N-(3-methylbenzyl)-L-prolinamide, Hirudin variant-1, SODIUM ION, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2007-12-18 | Release date: | 2008-11-04 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Exploring Thrombin S1 pocket To be Published
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4EB1
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![BU of 4eb1 by Molmil](/molmil-images/mine/4eb1) | Hyperstable in-frame insertion variant of antithrombin | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Antithrombin-III | Authors: | Martinez-Martinez, I, Johnson, D.J.D, Yamasaki, M, Corral, J, Huntington, J.A. | Deposit date: | 2012-03-23 | Release date: | 2012-07-18 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Type II antithrombin deficiency caused by a large in-frame insertion: structural, functional and pathological relevance. J.Thromb.Haemost., 10, 2012
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2B4X
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2UUF
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![BU of 2uuf by Molmil](/molmil-images/mine/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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5JZY
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![BU of 5jzy by Molmil](/molmil-images/mine/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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5AF9
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![BU of 5af9 by Molmil](/molmil-images/mine/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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4UEH
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![BU of 4ueh by Molmil](/molmil-images/mine/4ueh) | Thrombin in complex with benzamidine | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, BENZAMIDINE, GLYCEROL, ... | Authors: | Ruehmann, E, Heine, A, Klebe, G. | Deposit date: | 2014-12-17 | Release date: | 2015-08-26 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.16 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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4UDW
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![BU of 4udw by Molmil](/molmil-images/mine/4udw) | Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2, 5dichlorophenyl)methylpyrrolidine-2-carboxamide | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-(2,5-dichlorobenzyl)-L-prolinamide, GLYCEROL, ... | Authors: | Ruehmann, E, Heine, A, Klebe, G. | Deposit date: | 2014-12-12 | Release date: | 2015-08-26 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.16 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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4UE7
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![BU of 4ue7 by Molmil](/molmil-images/mine/4ue7) | Thrombin in complex with 1-amidinopiperidine | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | Authors: | Ruehmann, E, Heine, A, Klebe, G. | Deposit date: | 2014-12-16 | Release date: | 2015-08-26 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.129 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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4UD9
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![BU of 4ud9 by Molmil](/molmil-images/mine/4ud9) | Thrombin in complex with 5-chlorothiophene-2-carboxamide | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-CHLORO-2-THIOPHENECARBOXAMIDE, ... | Authors: | Ruehmann, E, Heine, A, Klebe, G. | Deposit date: | 2014-12-09 | Release date: | 2015-08-26 | Last modified: | 2024-01-31 | Method: | X-RAY DIFFRACTION (1.124 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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5AHG
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![BU of 5ahg by Molmil](/molmil-images/mine/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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2ODY
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![BU of 2ody by Molmil](/molmil-images/mine/2ody) | Thrombin-bound boophilin displays a functional and accessible reactive-site loop | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Boophilin, PHOSPHATE ION, ... | Authors: | Macedo-Ribeiro, S, Fuentes-Prior, P, Pereira, P.J.B. | Deposit date: | 2006-12-27 | Release date: | 2008-01-22 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Isolation, cloning and structural characterisation of boophilin, a multifunctional kunitz-type proteinase inhibitor from the cattle tick. Plos One, 3, 2008
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5DO4
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![BU of 5do4 by Molmil](/molmil-images/mine/5do4) | Thrombin-RNA aptamer complex | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Pallan, P.S, Egli, M. | Deposit date: | 2015-09-10 | Release date: | 2016-09-14 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.859 Å) | Cite: | Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res., 44, 2016
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5LPD
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![BU of 5lpd by Molmil](/molmil-images/mine/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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5AFY
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![BU of 5afy by Molmil](/molmil-images/mine/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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5AFZ
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![BU of 5afz by Molmil](/molmil-images/mine/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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2GDE
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![BU of 2gde by Molmil](/molmil-images/mine/2gde) | Thrombin in complex with inhibitor | Descriptor: | (R)-3-((2S,3R)-1-((2S,3AR,5S,6S,7AS)-2-(2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYLCARBAMOYL)-5,6-DIHYDROXYOCTAHYDRO-1H-INDOL-1-YL)-3-CHLORO-4-METHYL-1-OXOPENTAN-2-YLAMINO)-2-METHOXY-3-OXOPROPYL HYDROGEN SULFATE, Hirudin, SODIUM ION, ... | Authors: | Xue, Y. | Deposit date: | 2006-03-16 | Release date: | 2007-03-20 | Last modified: | 2013-03-13 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Total synthesis and structural confirmation of chlorodysinosin A. J.Am.Chem.Soc., 128, 2006
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5LCE
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![BU of 5lce by Molmil](/molmil-images/mine/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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6ROT
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![BU of 6rot by Molmil](/molmil-images/mine/6rot) | Thrombin in complex with MI2105 | Descriptor: | (2~{S})-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]-1-[2-[(phenylmethyl)sulfonylamino]ethanoyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | Authors: | Sandner, A, Heine, A, Klebe, G. | Deposit date: | 2019-05-13 | Release date: | 2019-11-27 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.339 Å) | Cite: | Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J.Med.Chem., 62, 2019
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2UUJ
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![BU of 2uuj by Molmil](/molmil-images/mine/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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5JFD
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![BU of 5jfd by Molmil](/molmil-images/mine/5jfd) | Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-arginyl)pyrrolidine-2-carboxamide | Descriptor: | (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]-1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | Authors: | Sandner, A, Heine, A, Klebe, G. | Deposit date: | 2016-04-19 | Release date: | 2017-05-24 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (1.46 Å) | Cite: | Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J.Med.Chem., 62, 2019
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2UUK
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![BU of 2uuk by Molmil](/molmil-images/mine/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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1NU7
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![BU of 1nu7 by Molmil](/molmil-images/mine/1nu7) | Staphylocoagulase-Thrombin Complex | Descriptor: | IMIDAZOLE, MERCURY (II) ION, N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, ... | Authors: | Friedrich, R, Bode, W, Fuentes-Prior, P, Panizzi, P, Bock, P.E. | Deposit date: | 2003-01-31 | Release date: | 2003-10-07 | Last modified: | 2012-12-12 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Staphylocoagulase is a prototype for the mechanism of cofactor-induced zymogen activation NATURE, 425, 2003
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6GBW
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![BU of 6gbw by Molmil](/molmil-images/mine/6gbw) | Thrombin in complex with MI2100 ((S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-L-arginyl)pyrrolidine-2-carboxamide) | Descriptor: | (2~{S})-~{N}-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2~{S})-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | Authors: | Sandner, A, Heine, A, Klebe, G. | Deposit date: | 2018-04-16 | Release date: | 2019-04-24 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J.Med.Chem., 62, 2019
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2JEW
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![BU of 2jew by Molmil](/molmil-images/mine/2jew) | |