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: | 2024-10-16 | 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
| 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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5L6N
| Disulfated madanin-thrombin complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Prothrombin, SODIUM ION, ... | Authors: | Ripoll-Rozada, J, Pereira, P.J.B. | Deposit date: | 2016-05-30 | Release date: | 2017-03-29 | Last modified: | 2024-10-16 | Method: | X-RAY DIFFRACTION (1.627 Å) | Cite: | Tyrosine sulfation modulates activity of tick-derived thrombin inhibitors. Nat Chem, 9, 2017
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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
| 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: | 2024-10-09 | 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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4LZ1
| X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 12 nucleobase | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, POTASSIUM ION, ... | Authors: | Pica, A, Russo Krauss, I, Merlino, A, Sica, F. | Deposit date: | 2013-07-31 | Release date: | 2014-01-08 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer. Febs J., 280, 2013
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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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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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1GHX
| A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE | Descriptor: | 2-(2-HYDROXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE, ACETYL HIRUDIN, CALCIUM ION, ... | Authors: | Katz, B.A, Elrod, K, Luong, C, Rice, M, Mackman, R.L, Sprengeler, P.A, Spencer, J, Hatayte, J, Janc, J, Link, J, Litvak, J, Rai, R, Rice, K, Sideris, S, Verner, E, Young, W. | Deposit date: | 2001-01-22 | Release date: | 2002-01-22 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. J.Mol.Biol., 307, 2001
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3PO1
| Thrombin in complex with Benzothiazole Guanidine | Descriptor: | ACETATE ION, SODIUM ION, Thrombin heavy chain, ... | Authors: | Xue, Y. | Deposit date: | 2010-11-21 | Release date: | 2011-11-23 | Last modified: | 2012-07-25 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Discovery of benzothiazole guanidines as novel inhibitors of thrombin and trypsin IV. Bioorg.Med.Chem.Lett., 22, 2012
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2ZIQ
| Thrombin Inhibition | Descriptor: | BENZAMIDINE, Hirudin variant-1, N-(4-carbamimidoylbenzyl)-1-(4-methylpentanoyl)-L-prolinamide, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2008-02-20 | Release date: | 2009-01-13 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Understanding Thrombin Inhibition To be Published
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1OYT
| COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED FLUORINATED INHIBITOR | Descriptor: | (3ASR,4RS,8ASR,8BRS)-4-(2-(4-FLUOROBENZYL)-1,3-DIOXODEACAHYDROPYRROLO[3,4-A] PYRROLIZIN-4-YL)BENZAMIDINE, CALCIUM ION, Hirudin IIB, ... | Authors: | Banner, D.W, Olsen, J.A. | Deposit date: | 2003-04-07 | Release date: | 2003-06-24 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.67 Å) | Cite: | A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of an Enzyme Active Site: Evidence for CF...C=O Interactions. Angew.Chem.Int.Ed.Engl., 42, 2003
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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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6EO6
| X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(2-(1H-indol-3-yl)acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, GA63A - TBA MODIFIED APTAMER, ... | Authors: | Dolot, R.M, Nawrot, B, Yang, X. | Deposit date: | 2017-10-09 | Release date: | 2017-10-25 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.69 Å) | Cite: | Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity. Nucleic Acids Res., 46, 2018
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2JH0
| Human Thrombin Hirugen Inhibitor complex | Descriptor: | (2R)-2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}PROPENE-1-SULFONAMIDE, CALCIUM ION, HIRUDIN IIIA, ... | Authors: | Senger, S, Chan, C, Convery, M.A, Hubbard, J.A, Young, R.J, Shah, G.P, Watson, N.S. | Deposit date: | 2007-02-19 | Release date: | 2007-05-08 | Last modified: | 2013-08-07 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Sulfonamide-Related Conformational Effects and Their Importance in Structure-Based Design. Bioorg.Med.Chem.Lett., 17, 2007
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5JDU
| Crystal structure for human thrombin mutant D189A | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, GLYCEROL, ... | Authors: | Pozzi, N, Chen, Z, Di Cera, E. | Deposit date: | 2016-04-17 | Release date: | 2016-07-13 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin. Biochemistry, 55, 2016
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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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6ZUH
| Crystal Structure of Thrombin in complex with compound17 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, Hirudin-2, ... | Authors: | Schafer, M. | Deposit date: | 2020-07-22 | Release date: | 2020-08-26 | Last modified: | 2024-05-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics. J.Med.Chem., 63, 2020
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6ZV8
| Crystal Structure of Thrombin in complex with compound51 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Hirudin-2, Prothrombin, ... | Authors: | Schafer, M. | Deposit date: | 2020-07-24 | Release date: | 2020-08-26 | Last modified: | 2024-05-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics. J.Med.Chem., 63, 2020
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3P6Z
| 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: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ... | Authors: | Corral-Rodriguez, M.A, Bock, P.E, Hernandez-Carvajal, E, Gutierrez-Gallego, R, Fuentes-Prior, P. | Deposit date: | 2010-10-11 | Release date: | 2011-06-15 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.7 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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6PXJ
| Crystal structure of human thrombin mutant I16T | Descriptor: | GLYCEROL, MAGNESIUM ION, Thrombin heavy chain, ... | Authors: | Stojanovski, B, Chen, Z, Koester, S.K, Pelc, L.A, Di Cera, E. | Deposit date: | 2019-07-26 | Release date: | 2019-12-18 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Role of the I16-D194 ionic interaction in the trypsin fold. Sci Rep, 9, 2019
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4RKJ
| Crystal structure of thrombin mutant S195T (free form) | Descriptor: | GLYCEROL, POTASSIUM ION, Thrombin heavy chain, ... | Authors: | Pelc, A.L, Chen, Z, Gohara, D.W, Vogt, A.D, Pozzi, N, Di Cera, E. | Deposit date: | 2014-10-13 | Release date: | 2015-03-11 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Why ser and not thr brokers catalysis in the trypsin fold. Biochemistry, 54, 2015
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2ZO3
| Bisphenylic Thrombin Inhibitors | Descriptor: | Hirudin variant-1, SODIUM ION, Thrombin heavy chain, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2008-05-05 | Release date: | 2009-04-14 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin J.Mol.Biol., 391, 2009
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2ZDV
| Exploring Thrombin S1 pocket | Descriptor: | D-phenylalanyl-N-(3-fluorobenzyl)-L-prolinamide, Hirudin variant-1, PHOSPHATE ION, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2007-11-29 | Release date: | 2008-10-28 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.72 Å) | Cite: | Exploring Thrombin S1 pocket To be Published
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2ZDA
| Exploring Thrombin S1 pocket | Descriptor: | D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide, Hirudin variant-1, PHOSPHATE ION, ... | Authors: | Baum, B, Heine, A, Klebe, G. | Deposit date: | 2007-11-21 | Release date: | 2008-10-28 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.73 Å) | Cite: | Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin J.Mol.Biol., 391, 2009
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