1P9A
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1RIW
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![BU of 1riw by Molmil](/molmil-images/mine/1riw) | Thrombin in complex with natural product inhibitor Oscillarin | Descriptor: | (2R,3AS,6R,7AS)-N-(2-{1-[AMINO(IMINO)METHYL]-2,5-DIHYDRO-1H-PYRROL-3-YL}ETHYL)-6-HYDROXY-1-{N-[(2S)-2-HYDROXY-3-PHENYLPROPANOYL]PHENYLALANYL}OCTAHYDRO-1H-INDOLE-2-CARBOXAMIDE, 2-acetamido-2-deoxy-beta-D-glucopyranose, Hirudin IIB, ... | Authors: | Hanessian, S, Tremblay, M, Petersen, J.F.W. | Deposit date: | 2003-11-18 | Release date: | 2004-11-09 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.04 Å) | Cite: | The N-acyloxyiminium ion aza-Prins route to octahydroindoles: total synthesis and structural confirmation of the antithrombotic marine natural product oscillarin J.Am.Chem.Soc., 126, 2004
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1NU9
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![BU of 1nu9 by Molmil](/molmil-images/mine/1nu9) | Staphylocoagulase-Prethrombin-2 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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2ZGB
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![BU of 2zgb by Molmil](/molmil-images/mine/2zgb) | Thrombin Inhibition | Descriptor: | D-leucyl-N-(3-chlorobenzyl)-L-prolinamide, Hirudin variant-1, SODIUM ION, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2008-01-21 | Release date: | 2008-12-16 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry. J.Mol.Biol., 397, 2010
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2ZHQ
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![BU of 2zhq by Molmil](/molmil-images/mine/2zhq) | Thrombin Inhibition | Descriptor: | Hirudin variant-1, N-(4-carbamimidoylbenzyl)-1-(3-phenylpropanoyl)-L-prolinamide, SODIUM ION, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2008-02-08 | Release date: | 2009-01-13 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.96 Å) | Cite: | Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry. J.Mol.Biol., 397, 2010
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2ZI2
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![BU of 2zi2 by Molmil](/molmil-images/mine/2zi2) | Thrombin Inhibition | Descriptor: | 1-butanoyl-N-(4-carbamimidoylbenzyl)-L-prolinamide, BENZAMIDINE, Hirudin variant-1, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2008-02-13 | Release date: | 2009-01-13 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry. J.Mol.Biol., 397, 2010
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2ZNK
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![BU of 2znk by Molmil](/molmil-images/mine/2znk) | Thrombin Inhibition | Descriptor: | D-leucyl-N-(4-carbamimidoylbenzyl)-L-prolinamide, Hirudin variant-1, SODIUM ION, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2008-04-26 | Release date: | 2009-04-14 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry. J.Mol.Biol., 397, 2010
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4MLF
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![BU of 4mlf by Molmil](/molmil-images/mine/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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5INW
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![BU of 5inw by Molmil](/molmil-images/mine/5inw) | Structure of reaction loop cleaved lamprey angiotensinogen | Descriptor: | C-terminal peptide of Putative angiotensinogen, Putative angiotensinogen, SULFATE ION | Authors: | Wei, H, Zhou, A. | Deposit date: | 2016-03-08 | Release date: | 2016-10-05 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Heparin Binds Lamprey Angiotensinogen and Promotes Thrombin Inhibition through a Template Mechanism J.Biol.Chem., 291, 2016
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1WAY
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![BU of 1way by Molmil](/molmil-images/mine/1way) | Active site thrombin inhibitors | Descriptor: | 4-[3-(4-CHLOROPHENYL)-1H-PYRAZOL-5-YL]PIPERIDINE, DIMETHYL SULFOXIDE, HIRUGEN, ... | Authors: | Hartshorn, M.J, Murray, C.W, Cleasby, A, Frederickson, M, Tickle, I.J, Jhoti, H. | Deposit date: | 2004-10-28 | Release date: | 2005-01-27 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.02 Å) | Cite: | Fragment-Based Lead Discovery Using X-Ray Crystallography J.Med.Chem., 48, 2005
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1WBG
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![BU of 1wbg by Molmil](/molmil-images/mine/1wbg) | Active site thrombin inhibitors | Descriptor: | 3-(4-CHLOROPHENYL)-5-(METHYLTHIO)-4H-1,2,4-TRIAZOLE, DIMETHYL SULFOXIDE, HIRUGEN, ... | Authors: | Hartshorn, M.J, Murray, C.W, Cleasby, A, Frederickson, M, Tickle, I.J, Jhoti, H. | Deposit date: | 2004-11-01 | Release date: | 2005-01-27 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Fragment-Based Lead Discovery Using X-Ray Crystallography J.Med.Chem., 48, 2005
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8TQS
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8BW5
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![BU of 8bw5 by Molmil](/molmil-images/mine/8bw5) | X-ray structure of the complex between human alpha thrombin and the duplex/quadruplex aptamer M08s-1_41mer | Descriptor: | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, M08s-1_41mer, N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Troisi, R, Napolitano, V, Sica, F. | Deposit date: | 2022-12-06 | Release date: | 2023-07-19 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide. Nucleic Acids Res., 51, 2023
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6GWE
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![BU of 6gwe by Molmil](/molmil-images/mine/6gwe) | Crystal structure of Thrombin bound to P2 macrocycle | Descriptor: | (10S,14S,17R)-14-(3-carbamimidamidopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(21),22,24-triene-17-carboxamide, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Cendron, L, Angelini, A, Kale, S.S, Bergeron-Brlek, M, Wu, Y, Heinis, C. | Deposit date: | 2018-06-23 | Release date: | 2019-09-25 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Thiol-to-amine cyclization reaction enables screening of large libraries of macrocyclic compounds and the generation of sub-kilodalton ligands. Sci Adv, 5, 2019
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5MJX
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![BU of 5mjx by Molmil](/molmil-images/mine/5mjx) | 2'F-ANA/DNA Chimeric TBA Quadruplex structure | Descriptor: | DNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3') | Authors: | Lietard, J, Abou Assi, H, Gomez-Pinto, I, Gonzalez, C, Somoza, M.M, Damha, M.J. | Deposit date: | 2016-12-02 | Release date: | 2017-02-01 | Last modified: | 2024-06-19 | Method: | SOLUTION NMR | Cite: | Mapping the affinity landscape of Thrombin-binding aptamers on 2 F-ANA/DNA chimeric G-Quadruplex microarrays. Nucleic Acids Res., 45, 2017
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6T0M
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![BU of 6t0m by Molmil](/molmil-images/mine/6t0m) | Cationic Trypsin 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, CALCIUM ION, Cationic trypsin, ... | Authors: | Ngo, K, Heine, A, Klebe, G. | Deposit date: | 2019-10-03 | Release date: | 2020-05-13 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.51 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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6SY3
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![BU of 6sy3 by Molmil](/molmil-images/mine/6sy3) | Cationic Trypsin in Complex with a D-DiPhe-Pro-pyridine derivative | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide, CALCIUM ION, Cationic Trypsin, ... | Authors: | Ngo, K, Heine, A, Klebe, G. | Deposit date: | 2019-09-27 | Release date: | 2020-05-13 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (0.95 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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6T5W
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![BU of 6t5w by Molmil](/molmil-images/mine/6t5w) | Cationic Trypsin in Complex with a D-Phe-Pro-p-aminopyridine Derivative (cocrystallizaton at 291 K) | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(6-azanylpyridin-3-yl)methyl]pyrrolidine-2-carboxamide, CALCIUM ION, Cationic Trypsin, ... | Authors: | Ngo, K, Heine, A, Klebe, G. | Deposit date: | 2019-10-17 | Release date: | 2020-05-13 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.13 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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6T0P
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![BU of 6t0p by Molmil](/molmil-images/mine/6t0p) | Cationic Trypsin 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, CALCIUM ION, Cationic Trypsin, ... | Authors: | Ngo, K, Heine, A, Klebe, G. | Deposit date: | 2019-10-03 | Release date: | 2020-05-13 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.19 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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6Z48
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![BU of 6z48 by Molmil](/molmil-images/mine/6z48) | Crystal structure of Thrombin in complex with macrocycle X1vE | Descriptor: | 5-chloranyl-N-[[(4S,15R)-2,5,13,16-tetrakis(oxidanylidene)-15-propan-2-yl-9,10-dithia-3,6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide, SODIUM ION, Thrombin heavy chain, ... | Authors: | Angelini, A, Habeshian, S, Heinis, C, Cendron, L. | Deposit date: | 2020-05-23 | Release date: | 2022-06-01 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (2.27 Å) | Cite: | Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale. Nat Commun, 13, 2022
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6T7H
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![BU of 6t7h by Molmil](/molmil-images/mine/6t7h) | Crystal structure of Thrombin in complex with macrocycle N14-PR4-A | Descriptor: | (14S,17R)-14-(3-carbamimidamidopropyl)-3-(furan-2-ylmethyl)-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(25),7,9,21,23-pentaene-17-carboxamide, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Angelini, A, Kumar, M.G, Heinis, C, Cendron, L. | Deposit date: | 2019-10-22 | Release date: | 2020-09-30 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (2.32 Å) | Cite: | Macrocycle synthesis strategy based on step-wise "adding and reacting" three components enables screening of large combinatorial libraries. Chem Sci, 11, 2020
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8EF4
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5XRF
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![BU of 5xrf by Molmil](/molmil-images/mine/5xrf) | Crystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus | Descriptor: | DI(HYDROXYETHYL)ETHER, Snake venom serine protease Da-36, alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Lin, C.-C, Wu, W.-G, Fan, Q, Tian, J, Zhang, Z, Zheng, Y. | Deposit date: | 2017-06-08 | Release date: | 2018-06-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus To Be Published
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3QGN
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![BU of 3qgn by Molmil](/molmil-images/mine/3qgn) | The allosteric E*-E equilibrium is a key property of the trypsin fold | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, IODIDE ION, ... | Authors: | Niu, W, Gohara, D, Chen, Z, Di Cera, E. | Deposit date: | 2011-01-24 | Release date: | 2011-07-06 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystallographic and kinetic evidence of allostery in a trypsin-like protease. Biochemistry, 50, 2011
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1MTS
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![BU of 1mts by Molmil](/molmil-images/mine/1mts) | FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN | Descriptor: | (+)-2-[4-[(-1-ACETIMIDOYL-4-PIPERIDINYL)OXY]-3-(7-AMIDINO-2-NAPHTHYL)PROPIONIC ACID, CALCIUM ION, TRYPSIN | Authors: | Stubbs, M.T. | Deposit date: | 1997-05-16 | Release date: | 1997-08-20 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin. FEBS Lett., 375, 1995
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