5AHG
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![BU of 5ahg by Molmil](/molmil-images/mine/5ahg) | Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine | 分子名称: | ((4-Chlorophenyl)sulfamoyl))dimethylamine, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | 著者 | Ruehmann, E, Heine, A, Klebe, G. | 登録日 | 2015-02-06 | 公開日 | 2015-08-26 | 最終更新日 | 2024-01-10 | 実験手法 | X-RAY DIFFRACTION (1.24 Å) | 主引用文献 | 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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6GBW
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![BU of 6gbw by Molmil](/molmil-images/mine/6gbw) | Thrombin in complex with MI2100 ((S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-L-arginyl)pyrrolidine-2-carboxamide) | 分子名称: | (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, ... | 著者 | Sandner, A, Heine, A, Klebe, G. | 登録日 | 2018-04-16 | 公開日 | 2019-04-24 | 最終更新日 | 2024-01-17 | 実験手法 | X-RAY DIFFRACTION (1.45 Å) | 主引用文献 | Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J.Med.Chem., 62, 2019
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5AF9
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![BU of 5af9 by Molmil](/molmil-images/mine/5af9) | Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide | 分子名称: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-methoxy-N-(pyridin-2-yl)benzamide, ... | 著者 | Ruehmann, E, Heine, A, Klebe, G. | 登録日 | 2015-01-20 | 公開日 | 2015-08-26 | 最終更新日 | 2024-01-10 | 実験手法 | X-RAY DIFFRACTION (1.18 Å) | 主引用文献 | 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
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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 | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Hirudin-2, N-(BENZYLSULFONYL)-D-PHENYLALANYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE, ... | 著者 | Ruehmann, E, Heine, A, Klebe, G. | 登録日 | 2015-01-27 | 公開日 | 2015-08-26 | 最終更新日 | 2024-01-31 | 実験手法 | X-RAY DIFFRACTION (1.53 Å) | 主引用文献 | 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
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![BU of 5afy by Molmil](/molmil-images/mine/5afy) | Thrombin in complex with 3-chloro-benzamide | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 3-CHLORO-BENZAMIDE, DIMETHYL SULFOXIDE, ... | 著者 | Ruehmann, E, Heine, A, Klebe, G. | 登録日 | 2015-01-27 | 公開日 | 2015-08-26 | 最終更新日 | 2024-01-31 | 実験手法 | X-RAY DIFFRACTION (1.12 Å) | 主引用文献 | 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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6GWE
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![BU of 6gwe by Molmil](/molmil-images/mine/6gwe) | Crystal structure of Thrombin bound to P2 macrocycle | 分子名称: | (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, ... | 著者 | Cendron, L, Angelini, A, Kale, S.S, Bergeron-Brlek, M, Wu, Y, Heinis, C. | 登録日 | 2018-06-23 | 公開日 | 2019-09-25 | 最終更新日 | 2024-01-17 | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | 主引用文献 | 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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5EDM
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![BU of 5edm by Molmil](/molmil-images/mine/5edm) | Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I ) | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | 著者 | Pozzi, N, Chen, Z, Di Cera, E. | 登録日 | 2015-10-21 | 公開日 | 2016-01-20 | 最終更新日 | 2023-11-15 | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | 主引用文献 | How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. J.Biol.Chem., 291, 2016
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3NXP
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![BU of 3nxp by Molmil](/molmil-images/mine/3nxp) | Crystal structure of human prethrombin-1 | 分子名称: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | 著者 | Chen, Z, Bush-Pelc, L.A, Di Cera, E. | 登録日 | 2010-07-14 | 公開日 | 2010-11-10 | 最終更新日 | 2023-09-06 | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | 主引用文献 | Crystal structure of prethrombin-1. Proc.Natl.Acad.Sci.USA, 107, 2010
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5A2M
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![BU of 5a2m by Molmil](/molmil-images/mine/5a2m) | Thrombin Inhibitor | 分子名称: | (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, ... | 著者 | Ruehmann, E, Heine, A, Klebe, G. | 登録日 | 2015-05-20 | 公開日 | 2016-06-01 | 最終更新日 | 2024-01-10 | 実験手法 | X-RAY DIFFRACTION (1.4 Å) | 主引用文献 | Thrombin Inhibition To be Published
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3P17
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![BU of 3p17 by Molmil](/molmil-images/mine/3p17) | Thrombin Inhibition by Pyridin Derivatives | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-(pyridin-3-ylmethyl)-L-prolinamide, Hirudin variant-2, ... | 著者 | Biela, A, Heine, A, Klebe, G. | 登録日 | 2010-09-30 | 公開日 | 2011-11-02 | 最終更新日 | 2023-12-06 | 実験手法 | X-RAY DIFFRACTION (1.43 Å) | 主引用文献 | Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin. J.Mol.Biol., 418, 2012
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3P70
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![BU of 3p70 by Molmil](/molmil-images/mine/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 | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BENZAMIDINE, ... | 著者 | Corral-Rodriguez, M.A, Bock, P.E, Hernandez-Carvajal, E, Gutierrez-Gallego, R, Fuentes-Prior, P. | 登録日 | 2010-10-11 | 公開日 | 2011-09-28 | 最終更新日 | 2023-09-06 | 実験手法 | X-RAY DIFFRACTION (2.55 Å) | 主引用文献 | 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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5EW1
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![BU of 5ew1 by Molmil](/molmil-images/mine/5ew1) | Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3 | 分子名称: | 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, ... | 著者 | Pica, A, Russo Krauss, I, Parente, V, Sica, F. | 登録日 | 2015-11-20 | 公開日 | 2016-11-30 | 最終更新日 | 2024-01-10 | 実験手法 | X-RAY DIFFRACTION (2.95 Å) | 主引用文献 | Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers. Nucleic Acids Res., 45, 2017
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5EW2
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![BU of 5ew2 by Molmil](/molmil-images/mine/5ew2) | Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT12 | 分子名称: | 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-deltaT12, ... | 著者 | Pica, A, Russo Krauss, I, Parente, V, Sica, F. | 登録日 | 2015-11-20 | 公開日 | 2016-11-30 | 最終更新日 | 2020-07-29 | 実験手法 | X-RAY DIFFRACTION (3.59 Å) | 主引用文献 | Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers. Nucleic Acids Res., 45, 2017
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3P6Z
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![BU of 3p6z by Molmil](/molmil-images/mine/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 | 分子名称: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ... | 著者 | Corral-Rodriguez, M.A, Bock, P.E, Hernandez-Carvajal, E, Gutierrez-Gallego, R, Fuentes-Prior, P. | 登録日 | 2010-10-11 | 公開日 | 2011-06-15 | 最終更新日 | 2024-03-13 | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | 主引用文献 | 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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7ZKM
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![BU of 7zkm by Molmil](/molmil-images/mine/7zkm) | X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form beta | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate, 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate, ... | 著者 | Troisi, R, Sica, F. | 登録日 | 2022-04-13 | 公開日 | 2022-11-30 | 最終更新日 | 2024-01-31 | 実験手法 | X-RAY DIFFRACTION (2 Å) | 主引用文献 | A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers. Mol Ther Nucleic Acids, 30, 2022
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7ZKN
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![BU of 7zkn by Molmil](/molmil-images/mine/7zkn) | X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form gamma | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate, 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate, ... | 著者 | Troisi, R, Sica, F. | 登録日 | 2022-04-13 | 公開日 | 2022-11-30 | 最終更新日 | 2024-01-31 | 実験手法 | X-RAY DIFFRACTION (3.03 Å) | 主引用文献 | A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers. Mol Ther Nucleic Acids, 30, 2022
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7ZKO
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![BU of 7zko by Molmil](/molmil-images/mine/7zko) | X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form delta | 分子名称: | 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate, 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, ... | 著者 | Troisi, R, Sica, F. | 登録日 | 2022-04-13 | 公開日 | 2022-11-30 | 最終更新日 | 2024-01-31 | 実験手法 | X-RAY DIFFRACTION (2.5 Å) | 主引用文献 | A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers. Mol Ther Nucleic Acids, 30, 2022
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7ZKL
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![BU of 7zkl by Molmil](/molmil-images/mine/7zkl) | X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form alpha | 分子名称: | (2S)-2-hydroxybutanedioic acid, 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate, 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate, ... | 著者 | Troisi, R, Sica, F. | 登録日 | 2022-04-13 | 公開日 | 2022-11-30 | 最終更新日 | 2024-01-31 | 実験手法 | X-RAY DIFFRACTION (3.18 Å) | 主引用文献 | A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers. Mol Ther Nucleic Acids, 30, 2022
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8ASE
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![BU of 8ase by Molmil](/molmil-images/mine/8ase) | Crystal structure of Thrombin in complex with macrocycle T3 | 分子名称: | (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, ... | 著者 | Chinellato, M, Angelini, A, Nielsen, A, Heinis, C, Cendron, L. | 登録日 | 2022-08-19 | 公開日 | 2023-11-29 | 実験手法 | X-RAY DIFFRACTION (2.55 Å) | 主引用文献 | Crystal structure of Thrombin in complex with optimized macrocycles T1 and T3 To Be Published
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8ASF
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![BU of 8asf by Molmil](/molmil-images/mine/8asf) | Crystal structure of Thrombin in complex with macrocycle T1 | 分子名称: | 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 | 著者 | Chinellato, M, Angelini, A, Nielsen, A, Heinis, C, Cendron, L. | 登録日 | 2022-08-19 | 公開日 | 2024-03-06 | 実験手法 | X-RAY DIFFRACTION (2.58 Å) | 主引用文献 | Crystal structure of Thrombin in complex with optimized macrocycles T1 and T3 To Be Published
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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 | 分子名称: | 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, ... | 著者 | Troisi, R, Napolitano, V, Sica, F. | 登録日 | 2022-12-06 | 公開日 | 2023-07-19 | 最終更新日 | 2023-09-20 | 実験手法 | X-RAY DIFFRACTION (2.8 Å) | 主引用文献 | Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide. Nucleic Acids Res., 51, 2023
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8BWW
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![BU of 8bww by Molmil](/molmil-images/mine/8bww) | |
2HWL
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![BU of 2hwl by Molmil](/molmil-images/mine/2hwl) | Crystal structure of thrombin in complex with fibrinogen gamma' peptide | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Fibrinogen gamma' peptide, Prothrombin, ... | 著者 | Pineda, A.O, Chen, Z.W, Marino, F, Mathews, F.S, Mosesson, M.W, Di Cera, E. | 登録日 | 2006-08-01 | 公開日 | 2006-09-19 | 最終更新日 | 2023-11-15 | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | 主引用文献 | Crystal structure of thrombin in complex with fibrinogen gamma' peptide. Biophys.Chem., 125, 2007
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2JH6
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![BU of 2jh6 by Molmil](/molmil-images/mine/2jh6) | Human Thrombin Hirugen Inhibitor complex | 分子名称: | 2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}ETHANESULFONAMIDE, CALCIUM ION, HIRUDIN IIIA, ... | 著者 | Senger, S, Chan, C, Convery, M.A, Hubbard, J.A, Young, R.J, Shah, G.P, Watson, N.S. | 登録日 | 2007-02-20 | 公開日 | 2007-05-08 | 最終更新日 | 2013-08-07 | 実験手法 | X-RAY DIFFRACTION (2.21 Å) | 主引用文献 | Sulfonamide-Related Conformational Effects and Their Importance in Structure-Based Design. Bioorg.Med.Chem.Lett., 17, 2007
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3VXF
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![BU of 3vxf by Molmil](/molmil-images/mine/3vxf) | X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5 | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, BIVALIRUDIN, Thrombin heavy chain, ... | 著者 | Yamada, T, Kurihara, K, Masumi, K, Tamada, T, Tomoyori, K, Ohnishi, Y, Tanaka, I, Kuroki, R, Niimura, N. | 登録日 | 2012-09-12 | 公開日 | 2013-09-04 | 最終更新日 | 2020-07-29 | 実験手法 | NEUTRON DIFFRACTION (1.602 Å), X-RAY DIFFRACTION | 主引用文献 | Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex Biochim.Biophys.Acta, 1834, 2013
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