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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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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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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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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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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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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3RM2
 | | Human Thrombin in complex with MI003 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | | Authors: | Biela, A, Heine, A, Klebe, G. | | Deposit date: | 2011-04-20 | | Release date: | 2012-04-25 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.23 Å) | | Cite: | Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect
J.Med.Chem., 55, 2012
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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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2BVR
 | | Human thrombin complexed with fragment-based small molecules occupying the S1 pocket | | Descriptor: | 2-[2-(4-CHLORO-PHENYLSULFANYL)-ACETYLAMINO]-3-(4-GUANIDINO-PHENYL)-PROPIONAMIDE, ALPHA THROMBIN, HIRUDIN VARIANT-2 | | Authors: | Neumann, T, Junker, H.-D, Keil, O, Burkert, K, Ottleben, H, Gamer, J, Sekul, R, Deppe, H, Feurer, A, Tomandl, D, Metz, G. | | Deposit date: | 2005-07-04 | | Release date: | 2006-10-25 | | Last modified: | 2016-12-21 | | Method: | X-RAY DIFFRACTION (1.25 Å) | | Cite: | Discovery of Thrombin Inhibitor Fragments from Chemical Microarray Screening
Lett.Drug Des.Discovery, 2, 2005
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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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3SI4
 | | Human Thrombin In Complex With UBTHR104 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(1-methylpyridinium-2-yl)methyl]-L-prolinamide, GLYCEROL, ... | | Authors: | Biela, A, Heine, A, Klebe, G. | | Deposit date: | 2011-06-17 | | Release date: | 2012-06-20 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.27 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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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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3SV2
 | | Human Thrombin In Complex With UBTHR105 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-(pyridin-4-ylmethyl)-L-prolinamide, GLYCEROL, ... | | Authors: | Biela, A, Heine, A, Klebe, G. | | Deposit date: | 2011-07-12 | | Release date: | 2012-06-20 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.3 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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2CN0
 | | Complex of Recombinant Human Thrombin with a Designed Inhibitor | | Descriptor: | 4-(1R,3AS,4R,8AS,8BR)-[1-DIFLUOROMETHYL-2-(4-FLUOROBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZAMIDINE, CALCIUM ION, HIRUDIN IIA, ... | | Authors: | Hoffmann-Roder, A, Schweizer, E, Egger, J, Seiler, P, Obst-Sander, U, Wagner, B, Kansy, M, Banner, D.W, Diederich, F. | | Deposit date: | 2006-05-17 | | Release date: | 2006-11-06 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Mapping the Fluorophilicity of a Hydrophobic Pocket: Synthesis and Biological Evaluation of Tricyclic Thrombin Inhibitors Directing Fluorinated Alkyl Groups Into the P Pocket
Chemmedchem, 1, 2006
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6T4A
 | | Thrombin in Complex with a D-Phe-Pro-p-aminopyridine derivative | | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(6-azanylpyridin-3-yl)methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | | Authors: | Ngo, K, Collins, C, Heine, A, Klebe, G. | | Deposit date: | 2019-10-13 | | Release date: | 2020-05-13 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.31 Å) | | Cite: | Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
J.Med.Chem., 63, 2020
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6T56
 | | Thrombin in Complex with Benzylamine | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, BENZYLAMINE, GLYCEROL, ... | | Authors: | Ngo, K, Abazi, N, Heine, A, Klebe, G. | | Deposit date: | 2019-10-15 | | Release date: | 2020-11-18 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.31 Å) | | Cite: | Thrombin in Complex with Benzylamine
To Be Published
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6YB6
 | | Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c) | | Descriptor: | 2-(aminomethyl)-5-chloranyl-benzene-1,4-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative, ... | | Authors: | Sandner, A, Heine, A, Klebe, G, Abazi, N. | | Deposit date: | 2020-03-16 | | Release date: | 2021-03-31 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.33 Å) | | Cite: | Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c)
To be published
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6YHG
 | | Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a) | | Descriptor: | 1-(3-methoxyphenyl)methanamine, 2-acetamido-2-deoxy-beta-D-glucopyranose, D-PHENYLALANINE, ... | | Authors: | Sandner, A, Heine, A, Klebe, G, Collins, C. | | Deposit date: | 2020-03-29 | | Release date: | 2021-04-07 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.33 Å) | | Cite: | Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)
To be published
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6T3Q
 | | Thrombin in Complex with a D-Phe-Pro-2-aminopyridine derivative | | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(2-azanylpyridin-4-yl)methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | | Authors: | Ngo, K, Collins, C, Heine, A, Klebe, G. | | Deposit date: | 2019-10-11 | | Release date: | 2020-05-13 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.33 Å) | | Cite: | Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
J.Med.Chem., 63, 2020
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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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3RM0
 | | Human Thrombin in complex with MI354 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | | Authors: | Biela, A, Heine, A, Klebe, G. | | Deposit date: | 2011-04-20 | | Release date: | 2012-04-25 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.34 Å) | | Cite: | Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect
J.Med.Chem., 55, 2012
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3QX5
 | | Thrombin Inhibition by Pyridin Derivatives | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-2-yl)methyl]-L-prolinamide, GLYCEROL, ... | | Authors: | Biela, A, Heine, A, Klebe, G. | | Deposit date: | 2011-03-01 | | Release date: | 2012-03-07 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.35 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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6T53
 | | Thrombin in Complex with a D-Phe-Pro-p-benzylamine derivative | | Descriptor: | (2~{S})-~{N}-[[4-(aminomethyl)phenyl]methyl]-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | | Authors: | Ngo, K, Abazi, N, Heine, A, Klebe, G. | | Deposit date: | 2019-10-15 | | Release date: | 2020-11-18 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Thrombin in Complex with a D-Phe-Pro-p-benzylamine derivative
To Be Published
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6T3M
 | | Thrombin in Complex with a D-Phe-Pro-p-phenol derivative | | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(4-hydroxyphenyl)methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, Hirudin variant-2, ... | | Authors: | Ngo, K, Collins, C, Heine, A, Klebe, G. | | Deposit date: | 2019-10-11 | | Release date: | 2020-11-18 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | Thrombin in Complex with a D-Phe-Pro-p-phenol derivative
To Be Published
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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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