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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6PX5
| CRYSTAL STRUCTURE OF HUMAN MEIZOTHROMBIN DESF1 MUTANT S195A bound with PPACK | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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, Prothrombin, ... | Authors: | Pelc, L.A, Koester, S.K, Chen, Z, Gistover, N, Di Cera, E. | Deposit date: | 2019-07-24 | Release date: | 2019-09-04 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Sci Rep, 9, 2019
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6PXQ
| Crystal structure of human thrombin mutant D194A | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Thrombin heavy chain, Thrombin light 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 (2.8 Å) | Cite: | Role of the I16-D194 ionic interaction in the trypsin fold. Sci Rep, 9, 2019
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8ASE
| Crystal structure of Thrombin in complex with macrocycle T3 | Descriptor: | (8~{S},14~{S},18~{E})-8-[(4-chlorophenyl)methyl]-3,21-dithia-7,10,16-triazatricyclo[21.2.2.1^{10,14}]octacosa-1(26),18,23(27),24-tetraene-6,9,15-trione, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Chinellato, M, Angelini, A, Nielsen, A, Heinis, C, Cendron, L. | Deposit date: | 2022-08-19 | Release date: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Crystal structure of Thrombin in complex with optimized macrocycles T1 and T3 To Be Published
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8ASF
| Crystal structure of Thrombin in complex with macrocycle T1 | Descriptor: | 5-chloranyl-~{N}-[[(9~{S},15~{R})-8,14,17-tris(oxidanylidene)-3,20-dithia-7,13,16-triazatetracyclo[20.2.2.1^{5,7}.1^{9,13}]octacosa-1(25),22(26),23-trien-15-yl]methyl]thiophene-2-carboxamide, Thrombin heavy chain, Thrombin light chain | Authors: | Chinellato, M, Angelini, A, Nielsen, A, Heinis, C, Cendron, L. | Deposit date: | 2022-08-19 | Release date: | 2024-03-06 | Method: | X-RAY DIFFRACTION (2.58 Å) | Cite: | Crystal structure of Thrombin in complex with optimized macrocycles T1 and T3 To Be Published
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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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5CMX
| X-ray structure of the complex between human alpha thrombin and a duplex/quadruplex 31-mer DNA aptamer | Descriptor: | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, POTASSIUM ION, RE31, ... | Authors: | Russo Krauss, I, Pica, A, Napolitano, V, Sica, F. | Deposit date: | 2015-07-17 | Release date: | 2016-01-13 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.98 Å) | Cite: | Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding. Nucleic Acids Res., 44, 2016
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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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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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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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8BWW
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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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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: | 2024-01-10 | 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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5E8E
| Crystal structure of thrombin bound to an exosite 1-specific IgA Fab | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CITRIC ACID, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, ... | Authors: | Baglin, T.P, Langdown, J, Frasson, R, Huntington, J.A. | Deposit date: | 2015-10-14 | Release date: | 2015-10-28 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Discovery and characterization of an antibody directed against exosite I of thrombin. J.Thromb.Haemost., 14, 2016
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5EDM
| Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I ) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | Authors: | Pozzi, N, Chen, Z, Di Cera, E. | Deposit date: | 2015-10-21 | Release date: | 2016-01-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. J.Biol.Chem., 291, 2016
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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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5EDK
| Crystal structure of prothrombin deletion mutant residues 146-167 ( Form II ). | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, ... | Authors: | Pozzi, N, Chen, Z, Di Cera, E. | Deposit date: | 2015-10-21 | Release date: | 2016-01-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (3.214 Å) | Cite: | How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. J.Biol.Chem., 291, 2016
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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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5Z5W
| VFR12 in complex with LPS micelles | Descriptor: | Peptide from Prothrombin | Authors: | Saravanan, R, Schmidtchen, A. | Deposit date: | 2018-01-21 | Release date: | 2018-03-07 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides. Nat Commun, 9, 2018
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5A2M
| Thrombin Inhibitor | Descriptor: | (2S)-1-[(2R)-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]-N-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | Authors: | Ruehmann, E, Heine, A, Klebe, G. | Deposit date: | 2015-05-20 | Release date: | 2016-06-01 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Thrombin Inhibition To be Published
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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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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
| 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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6GN7
| X-ray structure of the complex between human alpha thrombin and NU172, a duplex/quadruplex 26-mer DNA aptamer, in the presence of sodium ions. | Descriptor: | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, GLYCEROL, 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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Troisi, R, Russo Krauss, I, Sica, F. | Deposit date: | 2018-05-30 | Release date: | 2018-10-17 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer. Nucleic Acids Res., 46, 2018
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5EW1
| Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3 | 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, HD1-deltaT3, ... | Authors: | Pica, A, Russo Krauss, I, Parente, V, Sica, F. | Deposit date: | 2015-11-20 | Release date: | 2016-11-30 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers. Nucleic Acids Res., 45, 2017
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