3NXP
| Crystal structure of human prethrombin-1 | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | Authors: | Chen, Z, Bush-Pelc, L.A, Di Cera, E. | Deposit date: | 2010-07-14 | Release date: | 2010-11-10 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of prethrombin-1. Proc.Natl.Acad.Sci.USA, 107, 2010
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6EO9
| Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor | Descriptor: | DIMETHYL SULFOXIDE, Hirudin variant-2, N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-{3-[(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl)oxy]propoxy}phenyl)-1-(propan-2-yl)piperidine-4-carboxamide, ... | Authors: | Belviso, B.D, Caliandro, R, Aresta, B.M, De Candia, M, Altomare, C.D. | Deposit date: | 2017-10-09 | Release date: | 2017-12-13 | Last modified: | 2019-10-16 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | How a beta-D-glucoside side chain enhances binding affinity to thrombin of inhibitors bearing 2-chlorothiophene as P1 moiety: crystallography, fragment deconstruction study, and evaluation of antithrombotic properties. J. Med. Chem., 57, 2014
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6EVV
| X-ray structure of the complex between human alpha thrombin and NU172, a duplex/quadruplex 26-mer DNA aptamer, in the presence of potassium 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)-[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, Russo Krauss, I, Sica, F. | Deposit date: | 2017-11-02 | Release date: | 2018-10-24 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.5 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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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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3JZ2
| Crystal structure of human thrombin mutant N143P in E* form | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Thrombin heavy chain, ... | Authors: | Niu, W, Chen, Z, Bush-Pelc, L.A, Bah, A, Gandhi, P.S, Di Cera, E. | Deposit date: | 2009-09-22 | Release date: | 2009-10-20 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Mutant N143P reveals how Na+ activates thrombin J.Biol.Chem., 284, 2009
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3P70
| 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: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BENZAMIDINE, ... | Authors: | Corral-Rodriguez, M.A, Bock, P.E, Hernandez-Carvajal, E, Gutierrez-Gallego, R, Fuentes-Prior, P. | Deposit date: | 2010-10-11 | Release date: | 2011-09-28 | Last modified: | 2024-10-09 | Method: | X-RAY DIFFRACTION (2.55 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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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: | 2024-10-16 | 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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3K65
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3JZ1
| Crystal structure of human thrombin mutant N143P in E:Na+ form | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, NITRATE ION, ... | Authors: | Niu, W, Chen, Z, Bush-Pelc, L.A, Bah, A, Gandhi, P.S, Di Cera, E. | Deposit date: | 2009-09-22 | Release date: | 2009-10-20 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Mutant N143P reveals how Na+ activates thrombin J.Biol.Chem., 284, 2009
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8BWW
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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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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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6FJT
| 4-chloro-benzamidine in complex with thrombin | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-chloranylbenzenecarboximidamide, DIMETHYL SULFOXIDE, ... | Authors: | Abazi, N, Heine, A, Klebe, G. | Deposit date: | 2018-01-23 | Release date: | 2019-02-06 | Last modified: | 2024-10-16 | Method: | X-RAY DIFFRACTION (1.27 Å) | Cite: | 4-chloro-benzamidine in complex with thrombin To be published
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6EO8
| Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor | Descriptor: | DIMETHYL SULFOXIDE, Hirudin variant-2, N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-[3-(beta-D-glucopyranosyloxy)propoxy]phenyl)-1-(propan-2-yl)piperidine-4-carboxamide, ... | Authors: | Belviso, B.D, Caliandro, R, Aresta, B.M, De Candia, M, Altomare, C.D. | Deposit date: | 2017-10-09 | Release date: | 2017-12-13 | Last modified: | 2019-10-16 | Method: | X-RAY DIFFRACTION (1.94 Å) | Cite: | How a beta-D-glucoside side chain enhances binding affinity to thrombin of inhibitors bearing 2-chlorothiophene as P1 moiety: crystallography, fragment deconstruction study, and evaluation of antithrombotic properties. J. Med. Chem., 57, 2014
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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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6EO7
| X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(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, GA68B2 - MODIFIED HUMAN THROMBIN BINDING APTAMER, ... | Authors: | Dolot, R.M, Nawrot, B, Yang, X. | Deposit date: | 2017-10-09 | Release date: | 2017-10-18 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.24 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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3PMA
| 2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate | Descriptor: | 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose, CITRIC ACID, SODIUM ION, ... | Authors: | Wright, H.T, Scarsdale, J.N, Desai, B.J. | Deposit date: | 2010-11-16 | Release date: | 2011-07-20 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Interaction of thrombin with sucrose octasulfate. Biochemistry, 50, 2011
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3P17
| Thrombin Inhibition by Pyridin Derivatives | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-(pyridin-3-ylmethyl)-L-prolinamide, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2010-09-30 | Release date: | 2011-11-02 | Last modified: | 2024-10-09 | Method: | X-RAY DIFFRACTION (1.43 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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3PMH
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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: | 2024-10-16 | 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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3LDX
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3PMB
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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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3LU9
| Crystal structure of human thrombin mutant S195A in complex with the extracellular fragment of human PAR1 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Proteinase-activated receptor 1, ... | Authors: | Gandhi, P.S, Chen, Z, Di Cera, E. | Deposit date: | 2010-02-17 | Release date: | 2010-03-16 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structure of thrombin bound to the uncleaved extracellular fragment of PAR1. J.Biol.Chem., 285, 2010
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