3SHA
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![BU of 3sha by Molmil](/molmil-images/mine/3sha) | Human Thrombin In Complex With UBTHR97 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(4-chloropyridin-3-yl)methyl]-L-prolinamide, GLYCEROL, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-06-16 | Release date: | 2012-06-20 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.52 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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3QTO
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![BU of 3qto by Molmil](/molmil-images/mine/3qto) | Thrombin Inhibition by Pyridin Derivatives | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(1-methylpyridinium-3-yl)methyl]-L-prolinamide, GLYCEROL, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-02-23 | Release date: | 2012-02-29 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.52 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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3RML
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![BU of 3rml by Molmil](/molmil-images/mine/3rml) | Human Thrombin in complex with MI331 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-21 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.53 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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6TDT
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![BU of 6tdt by Molmil](/molmil-images/mine/6tdt) | Thrombin in Complex with a D-DiPhe-Pro-p-pyridine derivative | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | Authors: | Ngo, K, Heine, A, Klebe, G. | Deposit date: | 2019-11-10 | Release date: | 2020-05-13 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.53 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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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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1VZQ
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![BU of 1vzq by Molmil](/molmil-images/mine/1vzq) | Complex of thrombin with designed inhibitor 7165 | Descriptor: | 4-[(3AS,4R,7R,8AS,8BR)-2-(1,3-BENZODIOXOL-5-YLMETHYL)-7-HYDROXY-1,3-DIOXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZENECARBOXIMIDAMIDE, CALCIUM ION, HIRUDIN VARIANT-2, ... | Authors: | Shaerer, K, Morgenthaler, M, Seiler, P, Diederich, F, Banner, D.W, Tschopp, T, Obst-Sander, U. | Deposit date: | 2004-05-24 | Release date: | 2005-06-20 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (1.54 Å) | Cite: | Enantiomerically Pure Thrombin Inhibitors for Exploring the Molecular-Recognition Features of the Oxyanion Hole Helv.Chim.Acta, 87, 2004
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4UFF
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![BU of 4uff by Molmil](/molmil-images/mine/4uff) | Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl- propanamide | Descriptor: | (2R)-2-(benzylsulfonylamino)-N-(2-((4-carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl-propanamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-2, ... | Authors: | Ruehmann, E, Heine, A, Klebe, G. | Deposit date: | 2015-03-16 | Release date: | 2016-01-27 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures. Chemmedchem, 11, 2016
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3SI3
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![BU of 3si3 by Molmil](/molmil-images/mine/3si3) | Human Thrombin In Complex With UBTHR103 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-(pyridin-2-ylmethyl)-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 (1.55 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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6HSX
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![BU of 6hsx by Molmil](/molmil-images/mine/6hsx) | Thrombin in Complex with a D-Phe-Pro-diaminopyridine derivative | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[[2,6-bis(azanyl)pyridin-4-yl]methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | Authors: | Ngo, K, Heine, A, Klebe, G. | Deposit date: | 2018-10-02 | Release date: | 2019-10-23 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.56 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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6T54
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![BU of 6t54 by Molmil](/molmil-images/mine/6t54) | Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]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 (1.57 Å) | Cite: | Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative To Be Published
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6T57
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![BU of 6t57 by Molmil](/molmil-images/mine/6t57) | Thrombin in Complex with a D-Phe-Pro-N-amidinopiperidine Derivative | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(1-carbamimidoylpiperidin-4-yl)methyl]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: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.57 Å) | Cite: | Thrombin in Complex with a D-Phe-Pro-N-amidinopiperidine Derivative To Be Published
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3U9A
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![BU of 3u9a by Molmil](/molmil-images/mine/3u9a) | Human Thrombin In Complex With MI330 | Descriptor: | (2S)-N-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2S)-2-[(3-chloranyl-4-methoxy-phenyl)sulfonylamino]-4-[(4-cyanophenyl)methylamino]-4-oxidanylidene-butanoyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-10-18 | Release date: | 2012-10-24 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.58 Å) | Cite: | Thrombin Inhibition To be Published
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3RMM
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![BU of 3rmm by Molmil](/molmil-images/mine/3rmm) | Human Thrombin in complex with MI332 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-21 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.58 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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4UFE
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![BU of 4ufe by Molmil](/molmil-images/mine/4ufe) | Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-butyl)-3-phenyl-propanamide | Descriptor: | (2R)-N-[(2S)-1-[(4-carbamimidoylphenyl)methylamino]-1-oxidanylidene-propan-2-yl]-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-2, ... | Authors: | Ruehmann, E, Heine, A, Klebe, G. | Deposit date: | 2015-03-16 | Release date: | 2016-01-27 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.593 Å) | Cite: | Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures. Chemmedchem, 11, 2016
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5MLS
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![BU of 5mls by Molmil](/molmil-images/mine/5mls) | Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(3-chlorobenzyl)pyrrolidine-2-carboxamide | Descriptor: | D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide, DIMETHYL SULFOXIDE, GLYCEROL, ... | Authors: | Marca, A, Sandner, A, Heine, A, Klebe, G. | Deposit date: | 2016-12-07 | Release date: | 2017-12-20 | Last modified: | 2018-06-13 | Method: | X-RAY DIFFRACTION (1.62 Å) | Cite: | Thrombin Mutante A190S in complex with (S)-1-((R)-2-amino-3,3-diphenylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide to be published
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6T8A
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![BU of 6t8a by Molmil](/molmil-images/mine/6t8a) | Thrombin in complex with diphenyl ((4-carbamimidoylphenyl)((S)-1-((R)-3-cyclohexyl 2-((phenylmethyl)sulfonamido)propanoyl)pyrrolidine-2-carboxamido)methyl)phosphonate (MI-492) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, Hirudin variant-2, ... | Authors: | Ngaha, S.A, Sandner, A, Huber, S, Heine, A, Steinmetzer, T, Pilgram, O. | Deposit date: | 2019-10-24 | Release date: | 2020-11-18 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.62 Å) | Cite: | Thrombin in complex with diphenyl ((4-carbamimidoylphenyl)((S)-1-((R)-3-cyclohexyl-2-((phenylmethyl)sulfonamido)propanoyl)pyrrolidine-2-carboxamido)methyl)phosphonate (MI-492) to be published
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3QTV
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![BU of 3qtv by Molmil](/molmil-images/mine/3qtv) | Thrombin Inhibition by Pyridin Derivatives | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(1-methylpyridinium-4-yl)methyl]-L-prolinamide, GLYCEROL, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-02-23 | Release date: | 2012-02-29 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.63 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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4UFG
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![BU of 4ufg by Molmil](/molmil-images/mine/4ufg) | Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-((1S)-2-((4- carbamimidoylphenyl)methylamino)-1-methyl-2-oxo-ethyl)-N-methyl-3- phenyl-propanamide ethane | Descriptor: | (2S)-N-[(4-carbamimidoylphenyl)methyl]-2-[methyl-[(2R)-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanoyl]amino]butanamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-2, ... | Authors: | Ruehmann, E, Heine, A, Klebe, G. | Deposit date: | 2015-03-17 | Release date: | 2016-01-27 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures. Chemmedchem, 11, 2016
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1W7G
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![BU of 1w7g by Molmil](/molmil-images/mine/1w7g) | Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- Arginine template inhibitor CS107 | Descriptor: | HIRUDIN I, N-{(1S)-1-{[4-(3-AMINOPROPYL)PIPERAZIN-1-YL]CARBONYL}-4-[(DIAMINOMETHYLENE)AMINO]BUTYL}-3-(TRIFLUOROMETHYL)BENZENESULFONAMIDE, THROMBIN | Authors: | Remiche, J, Sauvage, E, Herman, R, Charlier, P. | Deposit date: | 2004-09-02 | Release date: | 2006-05-24 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Design, Synthesis and Evaluation of Graftable Thrombin Inhibitors for the Preparation of Blood-Compatible Polymer Materials. Org.Biomol.Chem., 3, 2005
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3RLW
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![BU of 3rlw by Molmil](/molmil-images/mine/3rlw) | Human Thrombin in complex with MI328 | 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 (1.69 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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1DOJ
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![BU of 1doj by Molmil](/molmil-images/mine/1doj) | Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, ALPHA-THROMBIN, HIRUGEN, ... | Authors: | Recacha, R, Costanzo, M.J, Maryanoff, B.E, Carson, M, DeLucas, L, Chattopadhyay, D. | Deposit date: | 1999-12-21 | Release date: | 2000-11-03 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structure of human alpha-thrombin complexed with RWJ-51438 at 1.7 A: unusual perturbation of the 60A-60I insertion loop. Acta Crystallogr.,Sect.D, 56, 2000
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3F68
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![BU of 3f68 by Molmil](/molmil-images/mine/3f68) | Thrombin Inhibition | Descriptor: | Hirudin variant-2, N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide, Prothrombin, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2008-11-05 | Release date: | 2009-10-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin. J.Mol.Biol., 391, 2009
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3QWC
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![BU of 3qwc by Molmil](/molmil-images/mine/3qwc) | Thrombin Inhibition by Pyridin Derivatives | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-3-yl)methyl]-L-prolinamide, GLYCEROL, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-02-28 | Release date: | 2012-03-14 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.75 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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2ZG0
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![BU of 2zg0 by Molmil](/molmil-images/mine/2zg0) | Exploring thrombin S3 pocket | Descriptor: | (S)-N-(4-carbamimidoylbenzyl)-1-(3-cyclohexylpropanoyl)pyrrolidine-2-carboxamide, Hirudin, SODIUM ION, ... | Authors: | Brandt, T, Baum, B, Heine, A, Klebe, G. | Deposit date: | 2008-01-16 | Release date: | 2009-01-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Exploring thrombin S3 pocket To be Published
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4LOY
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![BU of 4loy by Molmil](/molmil-images/mine/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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